US7425612B2 - Genes and polypeptides relating to human colon cancers - Google Patents

Genes and polypeptides relating to human colon cancers Download PDF

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US7425612B2
US7425612B2 US10/916,064 US91606404A US7425612B2 US 7425612 B2 US7425612 B2 US 7425612B2 US 91606404 A US91606404 A US 91606404A US 7425612 B2 US7425612 B2 US 7425612B2
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rnf43
cells
cxadrl1
gcud1
protein
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US20050069930A1 (en
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Yusuke Nakamura
Yoichi Furukawa
Hideaki Tahara
Takuya Tsunoda
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Oncotherapy Science Inc
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/04—Antineoplastic agents specific for metastasis
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4748—Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/32—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against translation products of oncogenes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer

Definitions

  • the present invention relates to the field of biological science, more specifically to the field of cancer research.
  • the present invention relates to novel genes, RNF43, CXADRL1, and GCUD1, involved in the proliferation mechanism of cells, as well as polypeptides encoded by the genes.
  • the genes and polypeptides of the present invention can be used, for example, in the diagnosis of cell proliferative disease, and as target molecules for developing drugs against the disease.
  • cDNA microarray technologies have enabled to obtain comprehensive profiles of gene expression in normal and malignant cells, and compare the gene expression in malignant and corresponding normal cells (Okabe et al., Cancer Res 61:2129-37 (2001); Kitahara et al., Cancer Res 61: 3544-9 (2001); Lin et al., Oncogene 21:4120-8 (2002); Hasegawa et al., Cancer Res 62:7012-7 (2002)).
  • This approach enables to disclose the complex nature of cancer cells, and helps to understand the mechanism of carcinogenesis. Identification of genes that are deregulated in tumors can lead to more precise and accurate diagnosis of individual cancers, and to develop novel therapeutic targets (Bienz and Clevers, Cell 103:311-20 (2000)).
  • FTIs farnesyltransferase
  • trastuzumab Clinical trials on human using a combination of anti-cancer drugs and anti-HER2 monoclonal antibody, trastuzumab, have been conducted to antagonize the proto-oncogene receptor HER2/neu; and have been achieving improved clinical response and overall survival of breast-cancer patients (Lin et al., Cancer Res 61:6345-9 (2001)).
  • a tyrosine kinase inhibitor, STI-571 which selectively inactivates bcr-abl fusion proteins, has been developed to treat chronic myelogenous leukemias wherein constitutive activation of bcr-abl tyrosine kinase plays a crucial role in the transformation of leukocytes.
  • Agents of these kinds are designed to suppress oncogenic activity of specific gene products (Fujita et al., Cancer Res 61:7722-6 (2001)). Therefore, gene products commonly up-regulated in cancerous cells may serve as potential targets for developing novel anti-cancer agents.
  • CTLs cytotoxic T lymphocytes
  • TAAs tumor-associated antigens
  • TAAs are now in the stage of clinical development as targets of immunotherapy. TAAs discovered so far include MAGE (van der Bruggen et al., Science 254: 1643-7 (1991)), gp100 (Kawakami et al., J Exp Med 180: 347-52 (1994)), SART (Shichijo et al., J Exp Med 187: 277-88 (1998)), and NY-ESO-1 (Chen et al., Proc Natl Acad Sci USA 94: 1914-8 (1997)). On the other hand, gene products which had been demonstrated to be specifically overexpressed in tumor cells, have been shown to be recognized as targets inducing cellular immune responses.
  • Such gene products include p53 (Umano et al., Brit J Cancer 84: 1052-7 (2001)), HER2/neu (Tanaka et al., Brit J Cancer 84: 94-9 (2001)), CEA (Nukaya et al., Int J Cancer 80: 92-7 (1999)), and so on.
  • TAAs In spite of significant progress in basic and clinical research concerning TAAs (Rosenbeg et al., Nature Med 4: 321-7 (1998); Mukherji et al., Proc Natl Acad Sci USA 92: 8078-82 (1995); Hu et al., Cancer Res 56: 2479-83 (1996)), only limited number of candidate TAAs for the treatment of adenocarcinomas, including colorectal cancer, are available. TAAs abundantly expressed in cancer cells, and at the same time which expression is restricted to cancer cells would be promising candidates as immunotherapeutic targets.
  • PBMCs peripheral blood mononuclear cells
  • HLA-A24 and HLA-A0201 are one of the popular HLA alleles in Japanese, as well as Caucasian (Date et al., Tissue Antigens 47: 93-101 (1996); Kondo et al., J Immunol 155: 4307-12 (1995); Kubo et al., J Immunol 152: 3913-24 (1994); Imanishi et al., Proceeding of the eleventh International Hictocompatibility Workshop and Conference Oxford University Press, Oxford, 1065 (1992); Williams et al., Tissue Antigen 49: 129 (1997)).
  • antigenic peptides of cancers presented by these HLAs may be especially useful for the treatment of cancers among Japanese and Caucasian.
  • An object of the present invention is to provide novel proteins involved in the proliferation mechanism of gastric or colorectal cancer cells and the genes encoding the proteins, as well as methods for producing and using the same in the diagnosis and treatment of gastric cancer or colorectal cancer.
  • the present inventors analyzed the expression-profiles of genes in gastric and colorectal carcinogenesis using a genome-wide cDNA microarray containing 23040 genes. From the pharmacological point of view, suppressing oncogenic signals is easier in practice than activating tumor-suppressive effects. Thus, the present inventors searched for genes that are up-regulated during gastric and colorectal carcinogenesis.
  • CXADRL1 coxsackie and adenovirus receptor like 1
  • GCUD1 up-regulated in gastric cancer
  • Gene transfer of CXADRL1 or GCUD1 promoted proliferation of cells.
  • reduction of CXADRL1 or GCUD1 expression by transfection of their specific antisense S-oligonucleotides or small interfering RNAs inhibited the growth of gastric cancer cells.
  • Many anticancer drugs such as inhibitors of DNA and/or RNA synthesis, metabolic suppressors, and DNA intercalators, are not only toxic to cancer cells but also for normally growing cells.
  • agents suppressing the expression of CXADRL1 may not adversely affect other organs due to the fact that normal expression of the gene is restricted to the testis and ovary, and thus may be of great importance for treating cancer.
  • gene RNF43 (Ring finger protein 43) assigned at chromosomal band 17pter-p 13.1 was identified.
  • yeast two-hybrid screening assay revealed that RNF43 protein associated with NOTCH2 or STRIN.
  • NOTCH2 is a large transmembrane receptor protein that is a component of an evolutionarily conserved intercellular signaling mechanism.
  • NOTCH2 is a protein member of the Notch signaling pathway and is reported to be involved in glomerulogenesis in the kidney and development of heart and eye vasculature (McCright et al., Development 128: 491-502 (2001)).
  • Three Delta/Serrate/Lag-2 (DSL) proteins, Delta1, Jaggaed1, and Jaggaed2 are reported as functional ligands for NOTCH2 (Shimizu et al., Mol Cell Biol 20: 6913-22 (2000)).
  • the signal induced by ligand binding in the Notch signaling pathway is transmitted intracellularly by a process involving proteolysis of the receptor and nuclear translocation of the intracellular domain of the NOTCH protein (see reviews Artavanis-Tsakonas et al., Annu Rev Cell Biol 7: 427-52 (1999); Weinmaster, Curr Opin Genet Dev 10: 363-9 (2000)).
  • reduction of RNF43 expression by transfection of specific antisense S-oligonucleotides or small interfering RNAs corresponding to RNF43 inhibited the growth of colorectal cancer cells.
  • many anticancer drugs are not only toxic to cancer cells but also for normally growing cells.
  • agents suppressing the expression of RNF43 may also not adversely affect other organs due to the fact that normal expression of the gene is restricted to fetus, more specifically fetal lung and fetal kidney, and thus may be of great importance for treating cancer.
  • the present invention provides isolated novel genes, CXADRL1, GCUD1, and RNF43, which are candidates as diagnostic markers for cancer as well as promising potential targets for developing new strategies for diagnosis and effective anti-cancer agents. Furthermore, the present invention provides polypeptides encoded by these genes, as well as the production and the use of the same. More specifically, the present invention provides the following:
  • the present application provides novel human polypeptides, CXADRL1, GCUD1, and RNF43, and functional equivalents thereof, that promote cell proliferation and is up-regulated in cell proliferative diseases, such as gastric and colorectal cancers.
  • the CXADRL1 polypeptide includes a putative 431 amino acid protein with about 37% identity to CXADR (coxsackie and adenovirus receptor).
  • CXADRL1 is encoded by the open reading frame of SEQ ID NO: 1 and contains two immunoglobulin domains at codons 29-124 and 158-232, as well as a transmembrane domain at codons 246-268.
  • the CXADRL1 polypeptide preferably includes the amino acid sequence set forth in SEQ ID NO: 2.
  • the present application also provides an isolated protein encoded from at least a portion of the CXADRL1 polynucleotide sequence, or polynucleotide sequences at least 30%, more preferably at least 40% complementary to the sequence set forth in SEQ ID NO: 1.
  • the GCUD1 polypeptide includes a putative 414 amino acid protein encoded by the open reading frame of SEQ ID NO: 3.
  • the GCUD1 polypeptide preferably includes the amino acid sequence set forth in SEQ ID NO: 4.
  • the present application also provides an isolated protein encoded from at least a portion of the GCUD1 polynucleotide sequence, or polynucleotide sequences at least 15%, more preferably at least 25% complementary to the sequence set forth in SEQ ID NO: 3.
  • the RNF43 polypeptide includes a putative 783 amino acid protein encoded by the open reading frame of SEQ ID NO: 5.
  • the RNF43 polypeptide preferably includes the amino acid sequence set forth in SEQ ID NO: 6 and contains a Ring finger motif at codons 272-312.
  • the RNF43 polypeptide showed 38% homology to RING finger protein homolog DKFZp566H073.1 (GenBank Accession Number: T08729).
  • the present application also provides an isolated protein encoded from at least a portion of the RNF43 polynucleotide sequence, or polynucleotide sequences at least 30%, more preferably at least 40% complementary to the sequence set forth in SEQ ID NO: 5.
  • the present invention further provides novel human genes, CXADRL1 and GCUD1, whose expressions are markedly elevated in a great majority of gastric cancers as compared to corresponding non-cancerous mucosae.
  • CXADRL1 and GCUD1 were also highly expressed in colorectal cancer and liver cancer.
  • the isolated CXADRL1 gene includes a polynucleotide sequence as described in SEQ ID NO: 1.
  • the CXADRL1 cDNA includes 3423 nucleotides that contain an open reading frame of 1296 nucleotides (SEQ ID NO: 1).
  • the present invention further encompasses polynucleotides which hybridize to and which are at least 30%, and more preferably at least 40% complementary to the polynucleotide sequence set forth in SEQ ID NO: 1, to the extent that they encode a CXADRL1 protein or a functional equivalent thereof.
  • polynucleotides are degenerates and allelic mutants of SEQ ID NO: 1.
  • the isolated GCUD1 gene includes a polynucleotide sequence as described in SEQ ID NO: 3.
  • the GCUD1 cDNA includes 4987 nucleotides that contain an open reading frame of 1245 nucleotides (SEQ ID NO: 3).
  • the present invention further encompasses polynucleotides which hybridize to and which are at least 15%, and more preferably at least 25% complementary to the polynucleotide sequence set forth in SEQ ID NO: 3, to the extent that they encode a GCUD1 protein or a functional equivalent thereof.
  • polynucleotides are degenerates and allelic mutants of SEQ ID NO: 3.
  • the present invention provides a novel human gene RNF43, whose expression is markedly elevated in a great majority of colorectal cancers as compared to corresponding non-cancerous mucosae.
  • RNF43 was also highly expressed in lung cancer, gastric cancer, and liver cancer.
  • the isolated RNF43 gene includes a polynucleotide sequence as described in SEQ ID NO: 5.
  • the RNF43 cDNA includes 5345 nucleotides that contain an open reading frame of 2352 nucleotides (SEQ ID NO: 5).
  • the present invention further encompasses polynucleotides which hybridize to and which are at least 30%, and more preferably at least 40% complementary to the polynucleotide sequence set forth in SEQ ID NO: 5, to the extent that they encode a RNF43 protein or a functional equivalent thereof.
  • polynucleotides are degenerates and allelic mutants of SEQ ID NO: 5.
  • an isolated gene is a polynucleotide whose structure is not identical to that of any naturally occurring polynucleotide or to that of any fragment of a naturally occurring genomic polynucleotide spanning more than three separate genes.
  • the term therefore includes, for example, (a) a DNA which has the sequence of part of a naturally occurring genomic DNA molecule in the genome of the organism in which it naturally occurs; (b) a polynucleotide incorporated into a vector or into the genomic DNA of a prokaryote or eukaryote in a manner such that the resulting molecule is not identical to any naturally occurring vector or genomic DNA; (c) a separate molecule such as a cDNA, a genomic fragment, a fragment produced by polymerase chain reaction (PCR), or a restriction fragment; and (d) a recombinant nucleotide sequence that is part of a hybrid gene, i.e., a gene encoding a fusion polypeptide.
  • the invention provides an isolated polynucleotide that encodes a polypeptide described herein or a fragment thereof.
  • the isolated polypeptide includes a nucleotide sequence that is at least 60% identical to the nucleotide sequence shown in SEQ ID NO: 1, 3, or 5. More preferably, the isolated nucleic acid molecule is at least 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, identical to the nucleotide sequence shown in SEQ ID NO: 1, 3, or 5.
  • an isolated polynucleotide which is longer than or equivalent in length to the reference sequence e.g., SEQ ID NO: 1, 3, or 5
  • the comparison is made with the full-length of the reference sequence.
  • the isolated polynucleotide is shorter than the reference sequence, e.g., shorter than SEQ ID NO: 1, 3, or 5
  • the comparison is made to segment of the reference sequence of the same length (excluding any loop required by the homology calculation).
  • the present invention also provides a method of producing a protein by transfecting or transforming a host cell with a polynucleotide sequence encoding the CXADRL1, GCUD1, or RNF43 protein, and expressing the polynucleotide sequence.
  • the present invention provides vectors comprising a nucleotide sequence encoding the CXADRL1, GCUD1, or RNF43 protein, and host cells harboring a polynucleotide encoding the CXADRL1, GCUD1, or RNF43 protein. Such vectors and host cells may be used for producing the CXADRL1, GCUD1, or RNF43 protein.
  • an antibody that recognizes the CXADRL1, GCUD1, or RNF43 protein is also provided by the present application.
  • an antisense polynucleotide e.g., antisense DNA
  • ribozyme e.g., ribozyme
  • siRNA small interfering RNA
  • the present invention further provides a method for diagnosis of cell proliferative diseases that includes determining an expression level of the gene in biological sample of specimen, comparing the expression level of CXADRL1, GCUD1, or RNF43 gene with that in normal sample, and defining a high expression level of the CXADRL1, GCUD1, or RNF43 gene in the sample as having a cell proliferative disease such as cancer.
  • the disease diagnosed by the expression level of CXADRL1 or GCUD1 is suitably a gastric, colorectal, and liver cancer; and that detected by the expression level of RNF43 is colorectal, lung, gastric, and liver cancer.
  • a method of screening for a compound for treating a cell proliferative disease includes the steps of contacting the CXADRL1, GCUD1, or RNF43 polypeptide with test compounds, and selecting test compounds that bind to the CXADRL1, GCUD1, or RNF43 polypeptide.
  • the present invention further provides a method of screening for a compound for treating a cell proliferative disease, wherein the method includes the steps of contacting the CXADRL1, GCUD1, or RNF43 polypeptide with a test compound, and selecting the test compound that suppresses the expression level or biological activity of the CXADRL1, GCUD1, or RNF43 polypeptide.
  • the present invention provides a method of screening for a compound for treating a cell proliferative disease, wherein the method includes the steps of contacting CXADRL1 and AIP1 in the presence of a test compound, and selecting the test compound that inhibits the binding of CXADRL1 and AIP1.
  • the present invention provides a method of screening for a compound for treating a cell proliferative disease, wherein the method includes the steps of contacting RNF43 and NOTCH2 or STRIN in the presence of a test compound, and selecting the test compound that inhibits the binding of RNF43 and NOTCH2 or STRIN.
  • the present application also provides a pharmaceutical composition for treating cell proliferative disease, such as cancer.
  • the pharmaceutical composition may be, for example, an anti-cancer agent.
  • the pharmaceutical composition can be described as at least a portion of the antisense S-oligonucleotides or siRNA of the CXADRL1, GCUD1, or RNF43 polynucleotide sequence shown and described in SEQ ID NO: 1, 3, or 5, respectively.
  • a suitable antisense S-oligonucleotide has the nucleotide sequence selected from the group of SEQ ID NO: 23, 25, 27, 29, or 31.
  • the antisense S-oligonucleotide of CXADRL1 including those having the nucleotide sequence of SEQ ID NO: 23 or 25 may be suitably used to treat gastric, colorectal and liver cancer; the antisense S-oligonucleotide of GCUD1 including those having the nucleotide sequence of SEQ ID NO: 27 or 29, suitably to treat gastric, colorectal, or liver cancer; and the antisense S-oligonucleotide of RNF43 including those having the nucleotide sequence of SEQ ID NO: 31, suitably for colorectal, lung, gastric, or liver cancer.
  • a suitable target sequence of siRNA has the nucleotide sequences selected from the group of SEQ ID NOs: 112, 113, or 114.
  • the target sequence of siRNA of CXADRL1 including those having the nucleotide sequence of SEQ ID NOs: 114 may be suitably used to treat gastric, colorectal, or liver cancer; and the target sequence of siRNA of RNF43 including those having the nucleotide sequence of SEQ ID NOs: 112, or 113, suitably for colorectal, lung, gastric, or liver cancer.
  • the pharmaceutical compositions may be also those comprising the compounds selected by the present methods of screening for compounds for treating cell proliferative diseases.
  • the course of action of the pharmaceutical composition is desirably to inhibit growth of the cancerous cells.
  • the pharmaceutical composition may be applied to mammals including humans and domestic mammals.
  • the present invention further provides methods for treating a cell proliferative disease using the pharmaceutical composition provided by the present invention.
  • the present invention provides method for treating or preventing cancer, which method comprises the step of administering the CXADRL1, GCUD1, or RNF43 polypeptide. It is expected that anti-tumor immunity be induced by the administration of the CXADRL1, GCUD1, or RNF43 polypeptide.
  • the present invention also provides method for inducing anti-tumor immunity, which method comprises the step of administering the CXADRL1, GCUD1, or RNF43 polypeptide, as well as pharmaceutical composition for treating or preventing cancer comprising the CXADRL1, GCUD1, or RNF43 polypeptide.
  • FIG. 1 a to 1 d depict the expression of A5928 (CXADRL1) and C8121 (GCUD1) in gastric cancers.
  • FIG. 1 a depicts the relative expression ratios (cancer/non-cancer) of A5928 in primary 14 gastric cancers examined by cDNA microarray. Its expression was up-regulated (Cy3:Cy5 intensity ratio, >2.0) in 14 of the 14 gastric cancers that passed through the cutoff filter (both Cy3 and Cy5 signals greater than 25,000).
  • FIG. 1 b depicts the relative expression ratios (cancer/non-cancer) of C8121 in primary 12 gastric cancers examined by cDNA microarray.
  • FIG. 1 c depicts the expression of CXADRL1 analyzed by semi-quantitative RT-PCR using 10 gastric cancer cases.
  • FIG. 1 d depicts the expression of GCUD1 analyzed by semi-quantitative RT-PCR using 9 gastric cancer cases. Expression of GAPDH served as an internal control for both the expression analyses of CXADRL1 and GCUD1.
  • FIGS. 2 a and 2 b depict the expression of CXADRL1 in various human tissues and the predicted protein structure and protein motifs of CXADRL1.
  • FIG. 2 a is a photograph depicting expression of CXADRL1 in various human tissues analyzed by multiple-tissue Northern-blot analysis.
  • FIG. 2 b depicts the predicted protein structure of CXADRL1.
  • the CXADRL1 cDNA consists of 3,423 nucleotides with an ORF of 1,296 nucleotides and is composed of 7 exons.
  • FIG. 3 a to 3 c depict the growth-promoting effect of CXADRL1.
  • FIG. 3 a is a photograph depicting the result of colony formation assays of NIH3T3 cells transfected with CXADRL1.
  • FIG. 3 b depicts the expression of exogeneous CXADRL1 in NIH3T3-CXADRL1 cells analyzed by semi-quantitative RT-PCR. Expression of GAPDH served as an internal control. #2, #5, #6, and #7 all indicate NIH3T3 cells transfected with CXADRL1.
  • FIG. 3 c depicts the number of NIH3T3 cells. Growth of NIH3T3-CXADRL1 cells was statistically higher than that of mock (NIH3T3-LacZ) cells in culture media containing 10% FBS (P ⁇ 0.05).
  • FIG. 4 depicts the growth-inhibitory effect of antisense S-oligonucleotides designated to suppress CXADRL1 in MKN-1 cells.
  • CXADRL1-AS4 and CXADRL1-AS5 were demonstrated to suppress the growth of MKN-1 cells.
  • FIG. 5A to 5C depict the growth suppressive effect of CXADRL1-siRNA on St-4 cells.
  • FIG. 5A presents photographs depicting the expression of CXADRL1 and GAPDH (control) in St-4 cells transfected with mock or CXADRL1-siRNA#7.
  • FIG. 5B depicts photographs depicting the result of Giemsa's staining of viable cells treated with control-siRNA or CXADRL1-siRNA#7.
  • FIG. 5C depicts the result of MTT assay on cells transfected with control plasmid or plasmids expressing CXADRL1-siRNA7.
  • FIG. 6 depicts a photograph demonstrating the result of immunoblot analysis of cells expressing exogeneous Flag-tagged CXADRL1 protein with anti-CXADRL1 antiserum or anti-Flag antibody.
  • FIG. 7 depicts the interaction between CXADRL1 and AIP1 examined by yeast two-hybrid system.
  • FIG. 7 is a photograph depicting the interaction of CXADRL1 with AIP1 examined by the two-hybrid system.
  • FIG. 8 depicts the peptide specific cytotoxicity of CTL line raised by CXADRL1-207 stimulation.
  • the CTL line showed high cytotoxic activity on target cells (T2) pulsed with CXADRL1-207, whereas no significant cytotoxic activity was detected on the same target cells (T2) pulsed without peptides.
  • FIG. 9 depicts the cytotoxic activity of CXADRL1-207 CTL Clone on SNU475, MKN74, and SNU-C4.
  • CXADRL1-207 CTL Clone showed high cytotoxic activity on SNU475 that expresses both CXADRL1 and HLA-A*0201.
  • CXADRL1-207 CTL Clone showed no significant cytotoxic activity on MKN74, which expresses CXADRL1 but not HLA-A*0201.
  • this CTL Clone did not show significant cytotoxic activity on SNU-C4, which expresses HLA-A*0201 but not CXADRL1.
  • FIG. 10 depicts the result of the cold target inhibition assay.
  • CXADRL1-207 CTL Clone specifically recognizes CXADRL1-207 in an HLA-A*0201 restricted manner.
  • SNU475 labeled with Na 2 51 Cr O 4 was prepared as a hot target, while CXADRL1-207 peptide-pulsed T2 (Peptide+) was used as a cold target (Inhibitors).
  • E/T ratio was fixed to 20.
  • the cytotoxic activity on SNU475 was inhibited by the addition of T2 pulsed with the identical peptide, while almost no inhibition by the addition of T2 without peptide pulse.
  • FIG. 11 depicts the result of the blocking assay showing the effect of antibodies raised against HLA-Class I, HLA-Class II, CD4, and CD8 on the cytotoxic activity of CXADRL1-207 CTL Clone.
  • CXADRL1-207 CTL Clone showed cytotoxic activity in HLA-Class I and CD8 restricted manner.
  • To examine the characteristics of CTL clone raised with CXADRL1 peptide antibodies against HLA-Class I, HLA-Class II, CD4, and CD8 were tested for their ability to inhibit the cytotoxic activity.
  • the horizontal axis reveals % inhibition of the cytotoxicity.
  • the cytotoxicity of CTL clone on SNU475 targets was significantly reduced when anti-class I and CD8 antibodies were used. This result indicates that the CTL clone recognizes the CXADRL1 derived peptide in a HLA-Class I and CD8 dependant manner.
  • FIG. 12 depicts the cytotoxic activities of CTLs induced with anchor modified peptide CXADRL1-9V.
  • the cytotoxic activities of CXADRL1-9V induced CTL line 5 (A) and CTL clone 69 (B) against peptide pulsed T2 cells (HLA-A*0201 positive cell line) and tumor cell lines were examined by 4h 51 Cr release assay.
  • Both the CTL line 5 and CTL clone 69 recognized not only CXADRL1-9V but also the parental peptide CXADRL1-9mer-207, equally or more sharply at a low E/T ratio in the CTL clone 69, and killed SNU475 cells expressing naturally processed wild-type peptide CXADRL1-9mer-207 on the HLA-A*0201 molecule (C).
  • FIG. 13 is a photograph depicting the result of Northern-blot analysis of GCUD1 in various human tissues.
  • the transcript of GCUD1 is approximately 5.0-kb by size.
  • FIG. 14 shows a photograph depicting the subcellular localization of GCUD1 observed by immunocytochemistry of cells transfected with pcDNA3.1 myc/His-GCUD1. cMyc-tagged GCUD1 protein expressed from the plasmid localized in the cytoplasm.
  • FIG. 15 is a photograph showing the growth-promoting effect of GCUD1 on NIH3T3 cells examined by colony formation assays.
  • FIG. 16 depicts the growth-inhibitory effect of antisense S-oligonucleotides designated to suppress GCUD1 on MKN-28 cells.
  • GCUD1-AS5 and GCUD1-AS8 were revealed to suppress the growth of MKN-28 cells.
  • FIG. 17 depicts a photograph showing the purification of recombinant GCUD1 protein.
  • FIG. 18 depicts a photograph demonstrating the result of immunoblot analysis of cells expressing exogenous Flag-tagged GCUD1 protein with anti-GCUD1 antiserum or anti-Flag antibody.
  • FIG. 19 depicts the peptide specific cytotosicity of CTL line raised by GCUD1-196 or GCUD1-272 stimulation.
  • the CTL line showed high cytotoxic activity on target cells (T2) pulsed with GCUD1-196 or GCUD1-272, whereas no significant cytotoxic activity was detected on the same target cells (T2) pulsed without peptides.
  • FIG. 20 depicts the cytotoxic activity of GCUD1-196 CTL Clone on SNU475 and MKN45.
  • GCUD1-196 CTL Clone showed high cytotoxic activity on SNU475 that expresses both GCUD1 and HLA-A*0201.
  • GCUD1-196 CTL Clone showed no significant cytotoxic activity on MKN45, which expresses GCUD1 but not HLA-A*0201.
  • FIG. 21 depicts the result of the cold target inhibition assay.
  • GCUD1-196 CTL Clone specifically recognizes GCUD1-196 in an HLA-A*0201 restricted manner.
  • SNU475 labeled with Na 2 51 Cr O 4 was prepared as a hot target, while GCUD1-196 peptide-pulsed T2 (Peptide+) was used as a cold target (Inhibitors).
  • E/T ratio was fixed to 20.
  • the cytotoxic activity on SNU475 was inhibited by the addition of T2 pulsed with the identical peptide, while almost no inhibition was observed by the addition of T2 without peptide pulse.
  • FIG. 22 depicts the result of the blocking assay showing the effect of antibodies raised against HLA-Class I, HLA-Class II, CD4, and CD8 on the cytotoxic activity of GCUD1-196 CTL Clone.
  • GCUD1-196 CTL Clone showed cytotoxic activity in HLA-Class I and CD8 restricted manner.
  • antibodies against HLA-Class I, HLA-Class II, CD4, and CD8 were tested for their ability to inhibit the cytotoxic activity.
  • the horizontal axis reveals % inhibition of the cytotoxicity.
  • the cytotoxicity of CTL clone on SNU475 targets was significantly reduced when anti-class I and CD8 antibodies were used. This result indicates that the CTL clone recognizes the GCUD1 derived peptide in a HLA Class I and CD8 dependent manner.
  • FIG. 23 depicts the cytotoxic activities of CTLs induced with anchor modified peptide GCUD1-9V.
  • the cytotoxic activities of GCUD1-9V induced CTL line 3 (A) and CTL clone 16 (B) against peptide pulsed T2 cells (HLA-A*0201 positive cell line) and tumor cell lines were examined by 4h 51 Cr release assay.
  • Both CTL line 3 and CTL clone 16 recognized not only GCUD1-9V but also the parental peptide GCUD1-196, equally or more sharply at a low E/T ratio in CTL clone 16, and killed SNU475 cells expressing naturally processed wild-type peptide GCUD1-196 on the HLA-A*0201 molecule (C).
  • FIGS. 24 a and 24 b depict the expression of FLJ20315 in colon cancer.
  • FIG. 24 a depicts the relative expression ratios (cancer/non-cancer) of FLJ20315 in 11 primary colon cancer cases examined by cDNA microarray. Its expression was up-regulated (Cy3:Cy5 intensity ratio, >2.0) in 10 of the 11 colon cancer cases that passed through the cut-off filter (both Cy3 and Cy5 signals greater than 25,000).
  • FIG. 24 b depicts the expression of FLJ20315 analyzed by semi-quantitative RT-PCR using additional 18 colon cancer cases (T, tumor tissue; N, normal tissue). Expression of GAPDH served as an internal control.
  • FIG. 25 a depicts a photograph showing the result of fetal-tissue Northern-blot analysis of RNF43 in various human fetal tissues.
  • FIG. 25 b depicts the predicted protein structure of RNF43.
  • FIGS. 26 a and 26 b show photographs depicting the subcellular localization of myc-tagged RNF43 protein.
  • FIG. 26 a is a photograph depicting the result of Western-blot analysis of myc-tagged RNF43 protein using extracts from COS7 cells transfected with either pcDNA3.1-myc/His-RNF43 or control plasmids (mock).
  • FIG. 26 b presents photographs of the transfected cells that were stained with mouse anti-myc antibody and visualized by FITC-conjugated secondary antibody. Nuclei were counter-stained with DAPI.
  • FIG. 27 a to 27 c depicts the effect of RNF43 on cell growth.
  • FIG. 27 a is a photograph depicting the result of colony formation assay of RNF43 in NIH3T3 cells.
  • FIG. 27 b presents photographs depicting the expression of RNF43 in mock (COS7-pcDNA) and COS7-RNF43 cells that was established by the transfection of COS7 cells with pcDNA-RNF43.
  • FIG. 27 c depicts the result of comparison on cell growth between COS7-RNF43 cells stably expressing exogenous RNF43 and mock cells.
  • FIGS. 28 a and 28 b depict the growth-inhibitory effect of antisense S-oligonucleotides designed to suppress RNF43.
  • FIG. 28 a presents photographs depicting the expression of RNF43 in LoVo cells treated for 12 h with either control (RNF43-S1) or antisense S-oligonucleotides (RNF43-AS1) analyzed by semi-quantitative RT-PCR.
  • FIG. 28 b depicts the cell viability of LoVo cells after treatment with the control or antisense S-oligonucleotides measured by MTT assay. The MTT assay was carried out in triplicate.
  • FIG. 29A to 29C depict the growth suppressive effect of RNF43-siRNAs.
  • FIG. 29A presents photographs depicting the effect of RNF43-siRNAs on the expression of RNF43.
  • FIG. 29B presents photographs depicting the result of Giemsa's staining of viable cells after the treatment with control-siRNA or RNF43-siRNAs.
  • FIG. 29C depicts the result of MTT assay on cells transfected with control plasmid or plasmids expressing RNF43-siRNAs. *, a significant difference (p ⁇ 0.05) as determined by a Fisher's protected least significant difference test.
  • FIGS. 30A and 30B depict the expression of tagged RNF43 protein.
  • FIG. 30A is a photograph depicting the result of Western-blot analysis of Flag-tagged RNF43 protein secreted in the culture media of COS7 cells transfected with pFLAG-5CMV-RNF43 (lane 2) or mock vector (lane 1).
  • FIG. 30B is a photograph depicting the result of Western-blot analysis of Myc-tagged RNF43 protein secreted in the culture media of COS7 cells transfected with pcDNA3.1-Myc/His-RNF43 (lane 2) or mock vector (lane 1).
  • FIGS. 31A and 31B depict the growth promoting effect of conditioned media containing the Myc-tagged or Flag-tagged RNF43 protein.
  • FIG. 31A presents photographs depicting the morphology of NIH3T3 cells cultured in control media (1) or in conditioned media of COS7 cells transfected with mock vector (2), pcDNA3.1-Myc/His-RNF43 (3), or pFLAG-5CMV-RNF43 (4).
  • FIG. 31B depicts the number of NIH3T3 cells cultured in the indicated media described in FIG. 31A . Data are shown as means of triplicate experiments for each group; bars, ⁇ SE. *, significant difference when compared with control, mock (p ⁇ 0.05).
  • FIG. 32A to 32C depict the preparation of N-terminal (N1) and C-terminal (C1) recombinant protein of RNF43.
  • FIG. 32A depicts the schematic structure of the recombinant protein RNF43-N1 and -C1.
  • FIG. 32B is a photograph depicting the expression of NusTM-tagged RNF43-N1 protein in E. coli with (lane2) or without (lane 1) 0.2 mM of IPTG.
  • FIG. 32C is a photograph depicting the expression of NusTM-tagged RNF43-C1 protein in E. coli with (lane2) or without (lane 1) 1 mM of IPTG.
  • FIGS. 33A and 33B depict the interaction between RNF43 and NOTCH2 examined by yeast two-hybrid system.
  • FIG. 33A depicts the predicted structure and the interacting region of NOTCH2.
  • (a) shows the predicted full-length structure of NOTCH2 protein, and
  • (b) shows the predicted responsible region for the interaction (ECD, Extracellular domain; TM, transmembrane domain; ICD, Intracellular domain).
  • FIG. 33B is a photograph depicting the interaction of RNF43 with NOTCH2 examined by the two-hybrid system.
  • FIGS. 34A and 34B depict the interaction between RNF43 and STRIN examined by the yeast two-hybrid system.
  • FIG. 34A depicts the predicted structure and the interacting region of STRIN. (a) shows the predicted full-length structure of STRIN protein, and (b) shows the predicted responsible region for the interaction (RING, RING domain).
  • FIG. 34B is a photograph depicting the interaction of RNF43 with STRIN examined by the two-hybrid system.
  • FIG. 35 depicts the peptide specific cytotoxicity of CTL line raised by RNF43-721 stimulation.
  • the CTL line showed high cytotoxic activity on target cells (TISI) pulsed with RNF43-721 (quadrilateral line), whereas no significant cytotoxic activity was detected on the same target cells (TISI) pulsed without peptides (triangular line).
  • CTL line was demonstrated to have a peptide specific cytotoxicity.
  • FIG. 36 depicts the peptide specific cytotoxicity of CTL clones raised by RNF43-721 stimulation.
  • the cytotoxic activity of 13 RNF43-721 CTL clones on peptide-pulsed targets (TISI) was tested as described under the item of “Materials and Methods”.
  • FIG. 37 depicts the cytotoxic activity of RNF43-721 CTL Clone 45 on HT29, WiDR and HCT116.
  • RNF43-721 CTL Clone recognizes and lyses tumor cells that endogenously express RNF43 in an HLA restricted fashion.
  • HT29, WiDR, and HCT116 all endogenously express RNF43, and RNF43-721 CTL Clone 45 served as an effector cell.
  • TISI was used as the target that does not express RNF43.
  • RNF43-721 CTL Clone 45 showed high cytotoxic activity on HT29 (filled triangular line) and WiDR (diamond line) that express both RNF43 and HLA-A24.
  • RNF43-721 CTL Clone 45 showed no significant cytotoxic activity on HCT116 (empty triangular line), which expresses RNF43 but not HLA-A24, and TISI (empty quadrilateral line), which expresses HLA-A24 but not RNF43. Moreover, RNF43-721 CTL Clone 45 showed no cytotoxic activity on irrelevant peptide pulsed TISI (filled quadrilateral dotted line) and SNU-C4 (filled circle line) which expresses RNF43 but little HLA-A24.
  • FIG. 38 depicts the result of the cold target inhibition assay.
  • RNF43-721 CTL Clone specifically recognizes RNF 43-721 in an HLA-A24 restricted manner.
  • HT29 labeled with Na 2 51 Cr O 4 was prepared as a hot target, while RNF43-721 peptide-pulsed TISI (Peptide+) was used as a cold target (Inhibitors). E/T ratio was fixed to 20.
  • the cytotoxic activity on HT29 was inhibited by the addition of TISI pulsed with the identical peptide (filled quadrilateral line), while almost no inhibition occurred by the addition of TISI without peptide pulsing (empty quadrilateral line).
  • FIG. 39 depicts the result of the blocking assay showing the effect of antibodies raised against HLA-Class I, HLA-Class II, CD3, CD4, and CD8 on the cytotoxic activity of RNF43-721 CTL Clone.
  • RNF43-721 CTL Clone showed cytotoxic activity in HLA-Class I, CD3, and CD8 restricted manner.
  • antibodies against HLA-Class I, HLA-Class II, CD3, CD4, and CD8 were tested for their ability to inhibit the cytotoxic activity.
  • the horizontal axis reveals % inhibition of the cytotoxicity.
  • the cytotoxicity of CTL clone on WiDR targets was significantly reduced when anti-class I, CD3, and CD8 antibodies were used. This result indicates that the CTL clone recognizes the RNF43 derived peptide in an HLA Class I, CD3, and CD8 dependent manner.
  • FIGS. 40A and 40B depict the peptide specific cytotoxicity of the CTL lines raised with RNF43-11-9 (A) or RNF43-11-10 (B). These CTL lines showed high cytotoxic activity on target cells (T2) pulsed with RNF43-11-9 or RNF43-11-10, whereas no significant cytotoxic activity was observed on the same target cells (T2) pulsed without peptides.
  • FIGS. 41A and 41B depict the peptide specific cytotoxicity of CTL clones raised by RNF43-11-9 stimulation. Cytotoxic activity of 4 RNF43-11-9 CTL clones on peptide-pulsed targets (T2) was tested as described under the item of “Materials and Methods”. The established RNF43-11-9 CTL clones had very potent cytotoxic activities on target cells (T2) pulsed with the peptides without showing any significant cytotoxic activity on the same target cells (T2) that were not pulsed with any peptides.
  • FIGS. 42A and 42B depict the cytotoxic activity of RNF43-5 CTL Clone 90 and RNF43-17 CTL Clone 25 on HT29 and DLD-1.
  • RNF43-5 CTL Clone 90 and RNF43-17 CTL Clone 25 recognize and lyse tumor cells that endogenously express RNF43 in an HLA restricted fashion.
  • HT29 and DLD-1 all endogenously express RNF43
  • RNF43-5 CTL Clone 90 and RNF43-17 CTL Clone 25 served as an effector cell.
  • T2 was used as the target that does not express RNF43.
  • RNF43-5 CTL Clone 90 and RNF43-17 CTL Clone 25 showed high cytotoxic activity on DLD-1 that express both RNF43 and HLA-A*0201.
  • RNF43-5 CTL Clone 90 and RNF43-17 CTL Clone 25 showed no significant cytotoxic activity on HT29, which expresses RNF43 but not HLA-A*0201.
  • FIG. 43 depicts the result of cold target inhibition assay.
  • RNF43 CTL Clone specifically recognizes RNF 43 in a HLA-A2 restricted manner.
  • HCT116 labeled with Na 2 51 Cr O 4 was prepared as a hot target, while RNF43 peptide-pulsed T2 (Peptide+) was used as a cold target (Inhibitors).
  • E/T ratio was fixed to 20.
  • the cytotoxic activity on HCT116 was inhibited by the addition of T2 pulsed with the identical peptide, while almost no inhibition was observed by the addition of TISI without peptide pulse.
  • the present application identifies novel human genes CXADRL1 and GCUD1 whose expression is markedly elevated in gastric cancer compared to corresponding non-cancerous tissues.
  • the CXADRL1 cDNA consists of 3423 nucleotides that contain an open reading frame of 1296 nucleotides as set forth in SEQ ID NO: 1. The open reading frame encodes a putative 431-amino acid protein.
  • CXADRL1 associates with atripin-1-interacting protein 1 (AIP1).
  • AIP1 is a protein that associates with atripin-1, a gene responsible for a hereditary disease, dentatorubral-pallidoluysian atrophy.
  • AIP1 encodes a deduced 1455-amino acid protein containing guanylate kinase-like domain, two WW domains and five PDZ domains.
  • the mouse homolog of AIP1 was shown to interact with activin type IIA. However, the function of AIP1 remains to be resolved.
  • the predicted amino acid sequence showed an identity of about 37% to coxsackie and adenovirus receptor (CXADR). Therefore this protein was dubbed coxsackie and adenovirus receptor like 1 (CXADRL1).
  • the GCUD1 cDNA consists of 4987 nucleotides that contain an open reading frame of 1245 nucleotides as set forth in SEQ ID NO: 3. The open reading frame encodes a putative 414-amino acid protein. Since the expression of the protein was up-regulated in gastric cancer, the protein was dubbed GCUD1 (up-regulated in gastric cancer).
  • the present invention encompasses novel human gene RNF43 whose expression is markedly elevated in colorectal cancer compared to corresponding non-cancerous tissue.
  • the RNF43 cDNA consists of 5345 nucleotides that contain an open reading frame of 2352 nucleotides as set forth in SEQ ID NO: 5. The open reading frame encodes a putative 783-amino acid protein.
  • RNF43 associates with NOTCH2 and STRIN.
  • NOTCH2 is reported as a large transmembrane receptor protein that is a component of an evolutionarily conserved intercellular signaling mechanism.
  • NOTCH2 is a protein member of the Notch signaling pathway and is reported to be involved in glomerulogenesis in the kidney and development of heart and eye vasculature.
  • STRIN encodes a putative protein that shares 79% identity with mouse Trif. The function of STRIN or Trif remains to be clarified.
  • the present invention encompasses novel human gene CXADRL1, including a polynucleotide sequence as described in SEQ ID NO: 1, as well as degenerates and mutants thereof, to the extent that they encode a CXADRL1 protein, including the amino acid sequence set forth in SEQ ID NO: 2 or its functional equivalent.
  • polypeptides functionally equivalent to CXADRL1 include, for example, homologous proteins of other organisms corresponding to the human CXADRL1 protein, as well as mutants of human CXADRL1 proteins.
  • the present invention also encompasses novel human gene GCUD1, including a polynucleotide sequence as described in SEQ ID NO: 3, as well as degenerates and mutants thereof, to the extent that they encode a GCUD1 protein, including the amino acid sequence set forth in SEQ ID NO: 4 or its functional equivalent.
  • polypeptides functionally equivalent to GCUD1 include, for example, homologous proteins of other organisms corresponding to the human GCUD1 protein, as well as mutants of human GCUD1 proteins.
  • the present invention encompasses novel human gene RNF43, including a polynucleotide sequence as described in SEQ ID NO: 5, as well as degenerates and mutants thereof, to the extent that they encode a RNF43 protein, including the amino acid sequence set forth in SEQ ID NO: 6 or its functional equivalent.
  • polypeptides functionally equivalent to RNF43 include, for example, homologous proteins of other organisms corresponding to the human RNF43 protein, as well as mutants of human RNF43 proteins.
  • the phrase “functionally equivalent” means that the subject polypeptide has activities to promote cell proliferation like CXADRL1, GCUD1, or RNF43 protein and to confer oncogenic activity to cancer cells. Whether the subject polypeptide has a cell proliferation activity or not can be judged by introducing the DNA encoding the subject polypeptide into a cell expressing the respective polypeptide, and detecting promotion of proliferation of the cells or increase in colony forming activity.
  • Such cells include, for example, NIH3T3 cells for CXADRL1 and GCUD1; and NIH3T3 cells, SW480 cells, and COS7 cells for RNF43.
  • whether the subject polypeptide is functionally equivalent to CXADRL1 may be judged by detecting its binding ability to AIP1.
  • whether the subject polypeptide is functionally equivalent to RNF43 may be judged by detecting its binding ability to NOTCH2 or STRIN.
  • polypeptides functionally equivalent to a given protein are well known by a person skilled in the art and include known methods of introducing mutations into the protein.
  • one skilled in the art can prepare polypeptides functionally equivalent to the human CXADRL1, GCUD1, or RNF43 protein by introducing an appropriate mutation in the amino acid sequence of either of these proteins by site-directed mutagenesis (Hashimoto-Gotoh et al., Gene 152:271-5 (1995); Zoller and Smith, Methods Enzymol 100: 468-500 (1983); Kramer et al., Nucleic Acids Res.
  • the polypeptide of the present invention includes proteins having the amino acid sequences of the human CXADRL1, GCUD1, or RNF43 protein in which one or more amino acids are mutated, provided the resulting mutated polypeptides are functionally equivalent to the human CXADRL1, GCUD1, or RNF43 protein.
  • the number of amino acids to be mutated in such a mutant is generally 10 amino acids or less, preferably 6 amino acids or less, and more preferably 3 amino acids or less.
  • Mutated or modified proteins proteins having amino acid sequences modified by substituting, deleting, inserting, and/or adding one or more amino acid residues of a certain amino acid sequence, have been known to retain the original biological activity (Mark et al., Proc Natl Acad Sci USA 81: 5662-6 (1984); Zoller and Smith, Nucleic Acids Res 10:6487-500 (1982); Dalbadie-McFarland et al., Proc Natl Acad Sci USA 79: 6409-13 (1982)).
  • the amino acid residue to be mutated is preferably mutated into a different amino acid in which the properties of the amino acid side-chain are conserved (a process known as conservative amino acid substitution).
  • properties of amino acid side chains are hydrophobic amino acids (A, I, L, M, F, P, W, Y, V), hydrophilic amino acids (R, D, N, C, E, Q, G, H, K, S, T), and side chains having the following functional groups or characteristics in common: an aliphatic side-chain (G, A, V, L, I, P); a hydroxyl group containing side-chain (S, T, Y); a sulfur atom containing side-chain (C, M); a carboxylic acid and amide containing side-chain (D, N, E, Q); a base containing side-chain (R, K, H); and an aromatic containing side-chain (H, F, Y, W).
  • the parenthetic letters indicate the one-letter codes of amino acids.
  • polypeptide to which one or more amino acids residues are added to the amino acid sequence of human CXADRL1, GCUD1, or RNF43 protein is a fusion protein containing the human CXADRL1, GCUD1, or RNF43 protein.
  • Fusion proteins are, fusions of the human CXADRL1, GCUD1, or RNF43 protein and other peptides or proteins, and are included in the present invention. Fusion proteins can be made by techniques well known to a person skilled in the art, such as by linking the DNA encoding the human CXADRL1, GCUD1, or RNF43 protein of the invention with DNA encoding other peptides or proteins, so that the frames match, inserting the fusion DNA into an expression vector and expressing it in a host. There is no restriction as to the peptides or proteins fused to the protein of the present invention.
  • peptides that can be used as peptides that are fused to the protein of the present invention include, for example, FLAG (Hopp et al., Biotechnology 6: 1204-10 (1988)), 6 ⁇ His containing six His (histidine) residues, 10 ⁇ His, Influenza agglutinin (HA), human c-myc fragment, VSP-GP fragment, p18HIV fragment, T7-tag, HSV-tag, E-tag, SV40T antigen fragment, Ick tag, ⁇ -tubulin fragment, B-tag, Protein C fragment, and the like.
  • FLAG Hopp et al., Biotechnology 6: 1204-10 (1988)
  • 6 ⁇ His containing six His (histidine) residues 10 ⁇ His
  • Influenza agglutinin (HA) Influenza agglutinin
  • human c-myc fragment VSP-GP fragment
  • p18HIV fragment T7-tag
  • HSV-tag HSV-tag
  • Fusion proteins can be prepared by fusing commercially available DNA, encoding the fusion peptides or proteins discussed above, with the DNA encoding the polypeptide of the present invention and expressing the fused DNA prepared.
  • polypeptides of the present invention include those that are encoded by DNA that hybridize with a whole or part of the DNA sequence encoding the human CXADRL1, GCUD1, or RNF43 protein and are functionally equivalent to the human CXADRL1, GCUD1, or RNF43 protein.
  • These polypeptides include mammal homologues corresponding to the protein derived from human (for example, a polypeptide encoded by a monkey, rat, rabbit or bovine gene). In isolating a cDNA highly homologous to the DNA encoding the human CXADRL1 protein from animals, it is particularly preferable to use tissues from testis or ovary.
  • tissue from testis, ovary, or brain in isolating a cDNA highly homologous to the DNA encoding the human GCUD1 from animals, it is particularly preferable to use tissues from testis, ovary, or brain. Further, in isolating a cDNA highly homologous to the DNA encoding the human RNF43 protein from animals, it is particularly preferable to use tissue from fetal lung or fetal kidney.
  • hybridization may be performed by conducting prehybridization at 68° C. for 30 min or longer using “Rapid-hyb buffer” (Amersham LIFE SCIENCE), adding a labeled probe, and warming at 68° C. for 1 hour or longer.
  • the following washing step can be conducted, for example, in a low stringent condition.
  • a low stringent condition is, for example, 42° C., 2 ⁇ SSC, 0.1% SDS, or preferably 50° C., 2 ⁇ SSC, 0.1% SDS.
  • high stringent conditions are used.
  • a high stringent condition is, for example, washing 3 times in 2 ⁇ SSC, 0.01% SDS at room temperature for 20 min, then washing 3 times in 1 ⁇ SSC, 0.1% SDS at 37° C. for 20 min, and washing twice in 1 ⁇ SSC, 0.1% SDS at 50° C. for 20 min.
  • temperature and salt concentration such as length of the probe and GC content of the probe, can influence the stringency of hybridization and one skilled in the art can suitably select the factors to achieve the requisite stringency.
  • a gene amplification method for example, the polymerase chain reaction (PCR) method, can be utilized to isolate a DNA encoding a polypeptide functionally equivalent to the human CXADRL1, GCUD1, or RNF43 protein, using a primer synthesized based on the sequence information of the protein encoding DNA (SEQ ID NO: 1, 3, or 5).
  • PCR polymerase chain reaction
  • Polypeptides that are functionally equivalent to the human CXADRL1, GCUD1, or RNF43 protein encoded by the DNA isolated through the above hybridization techniques or gene amplification techniques normally have a high homology to the amino acid sequence of the human CXADRL1, GCUD1, or RNF43 protein.
  • “High homology” typically refers to a homology of 40% or higher, preferably 60% or higher, more preferably 80% or higher, even more preferably 95% or higher.
  • the homology of a polypeptide can be determined by following the algorithm in “Wilbur and Lipman, Proc Natl Acad Sci USA 80: 726-30 (1983)”.
  • a polypeptide of the present invention may have variations in amino acid sequence, molecular weight, isoelectric point, the presence or absence of sugar chains, or form, depending on the cell or host used to produce it or the purification method utilized. Nevertheless, so long as it has a function equivalent to that of the human CXADRL1, GCUD1, or RNF43 protein of the present invention, it is within the scope of the present invention.
  • polypeptides of the present invention can be prepared as recombinant proteins or natural proteins, by methods well known to those skilled in the art.
  • a recombinant protein can be prepared by inserting a DNA, which encodes the polypeptide of the present invention (for example, the DNA comprising the nucleotide sequence of SEQ ID NO: 1, 3, or 5), into an appropriate expression vector, introducing the vector into an appropriate host cell, obtaining the extract, and purifying the polypeptide by subjecting the extract to chromatography, for example, ion exchange chromatography, reverse phase chromatography, gel filtration, or affinity chromatography utilizing a column to which antibodies against the protein of the present invention is fixed, or by combining more than one of the aforementioned columns.
  • chromatography for example, ion exchange chromatography, reverse phase chromatography, gel filtration, or affinity chromatography utilizing a column to which antibodies against the protein of the present invention is fixed, or by combining more than one of the aforementioned columns.
  • polypeptide of the present invention when expressed within host cells (for example, animal cells and E. coli ) as a fusion protein with glutathione-S-transferase protein or as a recombinant protein supplemented with multiple histidines, the expressed recombinant protein can be purified using a glutathione column or nickel column.
  • host cells for example, animal cells and E. coli
  • the polypeptide of the present invention is expressed as a protein tagged with c-myc, multiple histidines, or FLAG, it can be detected and purified using antibodies to c-myc, His, or FLAG, respectively.
  • a natural protein can be isolated by methods known to a person skilled in the art, for example, by contacting the affinity column, in which antibodies binding to the CXADRL1, GCUD1, or RNF43 protein described below are bound, with the extract of tissues or cells expressing the polypeptide of the present invention.
  • the antibodies can be polyclonal antibodies or monoclonal antibodies.
  • the present invention also encompasses partial peptides of the polypeptide of the present invention.
  • the partial peptide has an amino acid sequence specific to the polypeptide of the present invention and consists of at least 7 amino acids, preferably 8 amino acids or more, and more preferably 9 amino acids or more.
  • the partial peptide can be used, for example, for preparing antibodies against the polypeptide of the present invention, screening for a compound that binds to the polypeptide of the present invention, screening for accelerators or inhibitors of the polypeptide of the present invention, and as a tumor-associated antigen (TAA).
  • TAA tumor-associated antigen
  • a partial peptide of the invention can be produced by genetic engineering, by known methods of peptide synthesis, or by digesting the polypeptide of the invention with an appropriate peptidase.
  • peptide synthesis for example, solid phase synthesis or liquid phase synthesis may be used.
  • the present invention provides polynucleotides encoding the polypeptide of the present invention.
  • the polynucleotides of the present invention can be used for the in vivo or in vitro production of the polypeptide of the present invention as described above, or can be applied to gene therapy for diseases attributed to genetic abnormality in the gene encoding the protein of the present invention.
  • Any form of the polynucleotide of the present invention can be used so long as it encodes the polypeptide of the present invention, including mRNA, RNA, cDNA, genomic DNA, chemically synthesized polynucleotides.
  • the polynucleotide of the present invention include a DNA comprising a given nucleotide sequences as well as its degenerate sequences, so long as the resulting DNA encodes a polypeptide of the present invention.
  • the polynucleotide of the present invention can be prepared by methods known to a person skilled in the art.
  • the polynucleotide of the present invention can be prepared by: preparing a cDNA library from cells which express the polypeptide of the present invention, and conducting hybridization using a partial sequence of the DNA of the present invention (for example, SEQ ID NO: 1, 3, or 5) as a probe.
  • a cDNA library can be prepared, for example, by the method described in Sambrook et al., Molecular Cloning, Cold Spring Harbor Laboratory Press (1989); alternatively, commercially available cDNA libraries may be used.
  • a cDNA library can be also prepared by: extracting RNAs from cells expressing the polypeptide of the present invention, synthesizing oligo DNAs based on the sequence of the DNA of the present invention (for example, SEQ ID NO: 1, 3, or 5), conducting PCR using the oligo DNAs as primers, and amplifying cDNAs encoding the protein of the present invention.
  • the translation region encoded by the cDNA can be routinely determined, and the amino acid sequence of the polypeptide of the present invention can be easily obtained.
  • the genomic DNA library using the obtained cDNA or parts thereof as a probe, the genomic DNA can be isolated.
  • mRNAs may first be prepared from a cell, tissue, or organ (e.g., testis or ovary for CXADRL1; testis, ovary, or brain for GCUD1; and fetal lung, or fetal kidney for RNF43) in which the object polypeptide of the invention is expressed.
  • Known methods can be used to isolate mRNAs; for instance, total RNA may be prepared by guanidine ultracentrifugation (Chirgwin et al., Biochemistry 18:5294-9 (1979)) or AGPC method (Chomczynski and Sacchi, Anal Biochem 162:156-9 (1987)).
  • mRNA may be purified from total RNA using mRNA Purification Kit (Pharmacia) and such or, alternatively, mRNA may be directly purified by QuickPrep mRNA Purification Kit (Pharmacia).
  • cDNA is used to synthesize cDNA using reverse transcriptase.
  • cDNA may be synthesized using a commercially available kit, such as the AMV Reverse Transcriptase First-strand cDNA Synthesis Kit (Seikagaku Kogyo).
  • cDNA may be synthesized and amplified following the 5′-RACE method (Frohman et al., Proc Natl Acad Sci USA 85: 8998-9002 (1988); Belyavsky et al., Nucleic Acids Res 17: 2919-32 (1989)), which uses a primer and such, described herein, the 5′-Ampli FINDER RACE Kit (Clontech), and polymerase chain reaction (PCR).
  • 5′-RACE method Frohman et al., Proc Natl Acad Sci USA 85: 8998-9002 (1988); Belyavsky et al., Nucleic Acids Res 17: 2919-32 (1989)
  • a desired DNA fragment is prepared from the PCR products and ligated with a vector DNA.
  • the recombinant vectors are used to transform E. coli and such, and a desired recombinant vector is prepared from a selected colony.
  • the nucleotide sequence of the desired DNA can be verified by conventional methods, such as dideoxynucleotide chain termination.
  • the nucleotide sequence of a polynucleotide of the invention may be designed to be expressed more efficiently by taking into account the frequency of codon usage in the host to be used for expression (Grantham et al., Nucleic Acids Res 9: 43-74 (1981)).
  • the sequence of the polynucleotide of the present invention may be altered by a commercially available kit or a conventional method. For instance, the sequence may be altered by digestion with restriction enzymes, insertion of a synthetic oligonucleotide or an appropriate polynucleotide fragment, addition of a linker, or insertion of the initiation codon (ATG) and/or the stop codon (TAA, TGA, or TAG).
  • polynucleotide of the present invention encompasses the DNA comprising the nucleotide sequence of SEQ ID NO: 1, 3, or 5.
  • the present invention provides a polynucleotide that hybridizes under stringent conditions with a polynucleotide having a nucleotide sequence of SEQ ID NO: 1, 3, or 5, and encodes a polypeptide functionally equivalent to the CXADRL1, GCUD1, or RNF43 protein of the invention described above.
  • a stringent condition For example, low stringent condition can be used. More preferably, high stringent condition can be used. These conditions are the same as those described above.
  • the hybridizing DNA above is preferably a cDNA or a chromosomal DNA.
  • the present invention also provides a vector into which a polynucleotide of the present invention is inserted.
  • a vector of the present invention is useful to keep a polynucleotide, especially a DNA, of the present invention in host cell, to express the polypeptide of the present invention, or to administer the polynucleotide of the present invention for gene therapy.
  • E. coli When E. coli is a host cell and the vector is amplified and produced in a large amount in E. coli (e.g., JM109, DH5 ⁇ , HB101, or XL1Blue), the vector should have “ori” to be amplified in E. coli and a marker gene for selecting transformed E. coli (e.g., a drug-resistance gene selected by a drug such as ampicillin, tetracycline, kanamycin, chloramphenicol, or the like).
  • a marker gene for selecting transformed E. coli e.g., a drug-resistance gene selected by a drug such as ampicillin, tetracycline, kanamycin, chloramphenicol, or the like.
  • M13-series vectors, pUC-series vectors, pBR322, pBluescript, pCR-Script, etc. can be used.
  • pGEM-T pDIRECT
  • pT7 can also be used for subcloning and extracting cDNA as well as the vectors described above.
  • an expression vector is particularly useful.
  • an expression vector to be expressed in E. coli should have the above characteristics to be amplified in E. coli .
  • the vector should have a promoter, for example, lacZ promoter (Ward et al., Nature 341: 544-6 (1989); FASEB J 6: 2422-7 (1992)), araB promoter (Better et al., Science 240: 1041-3 (1988)), T7 promoter, or the like, that can efficiently express the desired gene in E. coli .
  • a promoter for example, lacZ promoter (Ward et al., Nature 341: 544-6 (1989); FASEB J 6: 2422-7 (1992)), araB promoter (Better et al., Science 240: 1041-3 (1988)), T7 promoter, or the like, that can efficiently express the desired gene in E. coli .
  • the host is preferably BL21 which expresses T7 RNA polymerase
  • the vector may also contain a signal sequence for polypeptide secretion.
  • An exemplary signal sequence that directs the polypeptide to be secreted to the periplasm of the E. coli is the pe1B signal sequence (Lei et al., J Bacteriol 169: 4379-83 (1987)).
  • Means for introducing of the vectors into the target host cells include, for example, the calcium chloride method, and the electroporation method.
  • expression vectors derived from mammals for example, pcDNA3 (Invitrogen) and pEGF-BOS (Mizushima et al., Nucleic Acids Res 18(17): 5322 (1990)), pEF, pCDM8), expression vectors derived from insect cells (for example, “Bac-to-BAC baculovirus expression system” (GIBCO BRL), pBacPAK8), expression vectors derived from plants (e.g., pMH1, pMH2), expression vectors derived from animal viruses (e.g., pHSV, pMV, pAdexLcw), expression vectors derived from retroviruses (e.g., pZIpneo), expression vector derived from yeast (e.g., “Pichia Expression Kit” (Invitrogen), pNV11, SP-Q01), and expression vectors derived from Bacillus subtilis (e.g., pcDNA3 (Invitrogen
  • the vector In order to express the vector in animal cells, such as CHO, COS, or NIH3T3 cells, the vector should have a promoter necessary for expression in such cells, for example, the SV40 promoter (Mulligan et al., Nature 277: 108-14 (1979)), the MMLV-LTR promoter, the EF1 ⁇ promoter (Mizushima et al., Nucleic Acids Res 18: 5322 (1990)), the CMV promoter, and the like; and preferably a marker gene for selecting transformants (for example, a drug resistance gene selected by a drug (e.g., neomycin, G418)).
  • a promoter necessary for expression in such cells for example, the SV40 promoter (Mulligan et al., Nature 277: 108-14 (1979)), the MMLV-LTR promoter, the EF1 ⁇ promoter (Mizushima et al., Nucleic Acids Res 18: 5322 (19
  • a vector comprising the complementary DHFR gene may be introduced into CHO cells in which the nucleic acid synthesizing pathway is deleted, and then amplified by methotrexate (MTX).
  • MTX methotrexate
  • the method wherein a vector comprising a replication origin of SV40 (pcD, etc.) is transformed into COS cells comprising the SV40 T antigen expressing gene on the chromosome can be used.
  • a polypeptide of the present invention obtained as above may be isolated from inside or outside (such as medium) of host cells, and purified as a substantially pure homogeneous polypeptide.
  • the phrase “substantially pure” as used herein in reference to a given polypeptide means that the polypeptide is substantially free from other biological macromolecules.
  • the substantially pure polypeptide is at least 75% (e.g., at least 80, 85, 95, or 99%) pure by dry weight. Purity can be measured by any appropriate standard method, for example, by column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis.
  • the method for polypeptide isolation and purification is not limited to any specific method; in fact, any standard method may be used.
  • column chromatography filter, ultrafiltration, salt precipitation, solvent precipitation, solvent extraction, distillation, immunoprecipitation, SDS-polyacrylamide gel electrophoresis, isoelectric point electrophoresis, dialysis, and recrystallization may be appropriately selected and combined to isolate and purify the polypeptide.
  • chromatography examples include, for example, affinity chromatography, ion-exchange chromatography, hydrophobic chromatography, gel filtration, reverse phase chromatography, adsorption chromatography, and such (Strategies for Protein Purification and Characterization: A Laboratory Course Manual. Ed. Daniel R. Marshak et al., Cold Spring Harbor Laboratory Press (1996)). These chromatographies may be performed by liquid chromatography, such as HPLC and FPLC. Thus, the present invention provides highly purified polypeptides prepared by the above methods.
  • a polypeptide of the present invention may be optionally modified or partially deleted by treating it with an appropriate protein modification enzyme before or after purification.
  • useful protein modification enzymes include, but are not limited to, trypsin, chymotrypsin, lysylendopeptidase, protein kinase, glucosidase, and so on.
  • the present invention provides an antibody that binds to the polypeptide of the invention.
  • the antibody of the invention can be used in any form, such as monoclonal or polyclonal antibodies, and includes antiserum obtained by immunizing an animal such as rabbit with the polypeptide of the invention, all classes of polyclonal and monoclonal antibodies, human antibodies, and humanized antibodies produced by genetic recombination.
  • a polypeptide of the invention used as an antigen to obtain an antibody may be derived from any animal species, but preferably is derived from a mammal such as human, mouse, or rat, more preferably from human.
  • a human-derived polypeptide may be obtained from the nucleotide or amino acid sequences disclosed herein.
  • the polypeptide to be used as an immunization antigen may be a complete protein or a partial peptide of the protein.
  • a partial peptide may comprise, for example, the amino (N)-terminal or carboxy (C)-terminal fragment of a polypeptide of the present invention.
  • a polypeptide of CXADRL1 encompassing the codons from 235 to 276, from 493 to 537, or from 70 to 111 can be used as partial peptides for producing antibodies against CXADRL1 of the present invention.
  • peptides comprising any one of following amino acid sequences may be used:
  • a gene encoding a polypeptide of the invention or its fragment may be inserted into a known expression vector, which is then used to transform a host cell as described herein.
  • the desired polypeptide or its fragment may be recovered from the outside or inside of host cells by any standard method, and may subsequently be used as an antigen.
  • whole cells expressing the polypeptide or their lysates, or a chemically synthesized polypeptide may be used as the antigen.
  • Any mammalian animal may be immunized with the antigen, but preferably the compatibility with parental cells used for cell fusion is taken into account.
  • animals of Rodentia, Lagomorpha, or Primates are used.
  • Animals of Rodentia include, for example, mouse, rat, and hamster.
  • Animals of Lagomorpha include, for example, rabbit.
  • Animals of Primates include, for example, a monkey of Catarrhini (old world monkey) such as Macaca fascicularis , rhesus monkey, sacred baboon, and chimpanzees.
  • antigens may be diluted and suspended in an appropriate amount of phosphate buffered saline (PBS), physiological saline, etc.
  • PBS phosphate buffered saline
  • the antigen suspension may be mixed with an appropriate amount of a standard adjuvant, such as Freund's complete adjuvant, made into emulsion, and then administered to mammalian animals.
  • a standard adjuvant such as Freund's complete adjuvant
  • an appropriately amount of Freund's incomplete adjuvant every 4 to 21 days.
  • An appropriate carrier may also be used for immunization.
  • serum is examined by a standard method for an increase in the amount of desired antibodies.
  • Polyclonal antibodies against the polypeptides of the present invention may be prepared by collecting blood from the immunized mammal examined for the increase of desired antibodies in the serum, and by separating serum from the blood by any conventional method.
  • Polyclonal antibodies include serum containing the polyclonal antibodies, as well as the fraction containing the polyclonal antibodies isolated from the serum.
  • Immunoglobulin G or M can be prepared from a fraction which recognizes only the polypeptide of the present invention using, for example, an affinity column coupled with the polypeptide of the present invention, and further purifying this fraction using protein A or protein G column.
  • immune cells are collected from the mammal immunized with the antigen and checked for the increased level of desired antibodies in the serum as described above, and are subjected to cell fusion.
  • the immune cells used for cell fusion are preferably obtained from spleen.
  • Other preferred parental cells to be fused with the above immunocyte include, for example, myeloma cells of mammals, and more preferably myeloma cells having an acquired property that enables selection of fused cells by drugs.
  • the above immunocyte and myeloma cells can be fused according to known methods, for example, the method of Milstein et al. (Galfre and Milstein, Methods Enzymol 73: 3-46 (1981)).
  • Resulting hybridomas obtained by the cell fusion may be selected by cultivating them in a standard selection medium, such as HAT medium (hypoxanthine, aminopterin, and thymidine containing medium).
  • HAT medium hyperxanthine, aminopterin, and thymidine containing medium.
  • the cell culture is typically continued in the HAT medium for several days to several weeks, the time being sufficient to allow all other cells, with the exception of the desired hybridoma (non-fused cells), to die. Then, the standard limiting dilution is performed to screen and clone a hybridoma cell producing the desired antibody.
  • human lymphocytes such as those infected by EB virus may be immunized with a polypeptide, polypeptide expressing cells, or their lysates in vitro. Then, the immunized lymphocytes are fused with human-derived myeloma cells that are capable of indefinitely dividing, such as U266, to yield a hybridoma producing a desired human antibody that is able to bind to the polypeptide can be obtained (Unexamined Published Japanese Patent Application No. (JP-A) Sho 63-17688).
  • the obtained hybridomas are subsequently transplanted into the abdominal cavity of a mouse and the ascites are extracted.
  • the obtained monoclonal antibodies can be purified by, for example, ammonium sulfate precipitation, a protein A or protein G column, DEAE ion exchange chromatography, or an affinity column to which the polypeptide of the present invention is coupled.
  • the antibody of the present invention can be used not only for purification and detection of the polypeptide of the present invention, but also is a candidate for agonists and antagonists of the polypeptide of the present invention.
  • this antibody can be applied to antibody treatment for diseases related to the polypeptide of the present invention.
  • a human antibody or a humanized antibody is preferable for reducing immunogenicity.
  • transgenic animals having a repertory of human antibody genes may be immunized with an antigen selected from a polypeptide, polypeptide expressing cells, or their lysates.
  • Antibody producing cells are then collected from the animals and fused with myeloma cells to obtain hybridoma, from which human antibodies against the polypeptide can be prepared (see WO92-03918, WO93-02227, WO94-02602, WO94-25585, WO96-33735, and WO96-34096).
  • an immune cell such as an immunized lymphocyte, producing antibodies may be immortalized by an oncogene and used for preparing monoclonal antibodies.
  • Monoclonal antibodies thus obtained can be also recombinantly prepared using genetic engineering techniques (see, for example, Borrebaeck and Larrick, Therapeutic Monoclonal Antibodies, published in the United Kingdom by MacMillan Publishers LTD (1990)).
  • a DNA encoding an antibody may be cloned from an immune cell, such as a hybridoma or an immunized lymphocyte producing the antibody, inserted into an appropriate vector, and introduced into host cells to prepare a recombinant antibody.
  • the present invention also provides recombinant antibodies prepared as described above.
  • an antibody of the present invention may be a fragment of an antibody or modified antibody, so long as it binds to one or more of the polypeptides of the invention.
  • the antibody fragment may be Fab, F(ab′) 2 , Fv, or single chain Fv (scFv), in which Fv fragments from H and L chains are ligated by an appropriate linker (Huston et al., Proc Natl Acad Sci USA 85: 5879-83 (1988)). More specifically, an antibody fragment may be generated by treating an antibody with an enzyme, such as papain or pepsin.
  • a gene encoding the antibody fragment may be constructed, inserted into an expression vector, and expressed in an appropriate host cell (see, for example, Co et al., J Immunol 152: 2968-76 (1994); Better and Horwitz, Methods Enzymol 178: 476-96 (1989); Pluckthun and Skerra, Methods Enzymol 178: 497-515 (1989); Lamoyi, Methods Enzymol 121: 652-63 (1986); Rousseaux et al., Methods Enzymol 121: 663-9 (1986); Bird and Walker, Trends Biotechnol 9: 132-7 (1991)).
  • An antibody may be modified by conjugation with a variety of molecules, such as polyethylene glycol (PEG).
  • PEG polyethylene glycol
  • the present invention further provides such modified antibodies.
  • the modified antibody can be obtained by chemically modifying an antibody. These modification methods are conventional in the field.
  • an antibody of the present invention may be obtained as a chimeric antibody, between a variable region derived from nonhuman antibody and the constant region derived from human antibody, or as a humanized antibody, comprising the complementarity determining region (CDR) derived from nonhuman antibody, the frame work region (FR) derived from human antibody, and the constant region.
  • CDR complementarity determining region
  • FR frame work region
  • Antibodies obtained as above may be purified to homogeneity.
  • the separation and purification of the antibody can be performed according to separation and purification methods used for general proteins.
  • the antibody may be separated and isolated by appropriately selected and combined use of column chromatographies, such as affinity chromatography, filter, ultrafiltration, salting-out, dialysis, SDS polyacrylamide gel electrophoresis, isoelectric focusing, and others (Antibodies: A Laboratory Manual. Ed Harlow and David Lane, Cold Spring Harbor Laboratory (1988)), but are not limited thereto.
  • a protein A column and protein G column can be used as the affinity column.
  • Exemplary protein A columns to be used include, for example, Hyper D, POROS, and Sepharose F.F. (Pharmacia).
  • Exemplary chromatography with the exception of affinity includes, for example, ion-exchange chromatography, hydrophobic chromatography, gel filtration, reverse-phase chromatography, adsorption chromatography, and the like (Strategies for Protein Purification and Characterization: A Laboratory Course Manual. Ed Daniel R. Marshak et al., Cold Spring Harbor Laboratory Press (1996)).
  • the chromatographic procedures can be carried out by liquid-phase chromatography, such as HPLC, and FPLC.
  • ELISA enzyme-linked immunosorbent assay
  • EIA enzyme immunoassay
  • RIA radioimmunoassay
  • the antibody of the present invention is immobilized on a plate, a polypeptide of the invention is applied to the plate, and then a sample containing a desired antibody, such as culture supernatant of antibody producing cells or purified antibodies, is applied. Then, a secondary antibody that recognizes the primary antibody and is labeled with an enzyme, such as alkaline phosphatase, is applied, and the plate is incubated.
  • a desired antibody such as culture supernatant of antibody producing cells or purified antibodies
  • an enzyme substrate such asp-nitrophenyl phosphate
  • the absorbance is measured to evaluate the antigen binding activity of the sample.
  • a fragment of the polypeptide such as a C terminal or N-terminal fragment, may be used as the antigen to evaluate the binding activity of the antibody.
  • BIAcore Pharmacia
  • the above methods allow for the detection or measurement of the polypeptide of the invention, by exposing the antibody of the invention to a sample assumed to contain the polypeptide of the invention, and detecting or measuring the immune complex formed by the antibody and the polypeptide.
  • the method of detection or measurement of the polypeptide according to the invention can specifically detect or measure a polypeptide, the method may be useful in a variety of experiments in which the polypeptide is used.
  • the present invention also provides a polynucleotide which hybridizes with the polynucleotide encoding human CXADRL1, GCUD1, or RNF43 protein (SEQ ID NO: 1, 3, or 5) or the complementary strand thereof, and which comprises at least 15 nucleotides.
  • the polynucleotide of the present invention is preferably a polynucleotide which specifically hybridizes with the DNA encoding the polypeptide of the present invention.
  • the phrase “specifically hybridize” as used herein, means that cross-hybridization does not occur significantly with DNA encoding other proteins, under the usual hybridizing conditions, preferably under stringent hybridizing conditions.
  • polynucleotides include, probes, primers, nucleotides and nucleotide derivatives (for example, antisense oligonucleotides and ribozymes), which specifically hybridize with DNA encoding the polypeptide of the invention or its complementary strand.
  • polynucleotide can be utilized for the preparation of DNA chip.
  • the present invention includes an antisense oligonucleotide that hybridizes with any site within the nucleotide sequence of SEQ ID NO: 1, 3, or 5.
  • This antisense oligonucleotide is preferably against at least 15 continuous nucleotides of the nucleotide sequence of SEQ ID NO: 1, 3, or 5.
  • the above-mentioned antisense oligonucleotide which contains an initiation codon in the above-mentioned at least 15 continuous nucleotides, is even more preferred.
  • antisense oligonucleotides include those comprising the nucleotide sequence of SEQ ID NO: 23 or 25 for suppressing the expression of CXADRL1; SEQ ID NO: 27, or 29 for GCUD1; and SEQ ID NO: 31 for RNF43.
  • Derivatives or modified products of antisense oligonucleotides can be used as antisense oligonucleotides.
  • modified products include lower alkyl phosphonate modifications, such as methyl-phosphonate-type or ethyl-phosphonate-type, phosphorothioate modifications and phosphoroamidate modifications.
  • antisense oligonucleotides means, not only those in which the nucleotides corresponding to those constituting a specified region of a DNA or mRNA are entirely complementary, but also those having a mismatch of one or more nucleotides, as long as the DNA or mRNA and the antisense oligonucleotide can specifically hybridize with the nucleotide sequence of SEQ ID NO: 1, 3, or 5.
  • Such polynucleotides are contained as those having, in the “at least 15 continuous nucleotide sequence region”, a homology of at least 70% or higher, preferably at 80% or higher, more preferably 90% or higher, even more preferably 95% or higher.
  • the algorithm stated herein can be used to determine the homology.
  • Such polynucleotides are useful as probes for the isolation or detection of DNA encoding the polypeptide of the invention as stated in a later example or as a primer used for amplifications.
  • the antisense oligonucleotide derivatives of the present invention act upon cells producing the polypeptide of the invention by binding to the DNA or mRNA encoding the polypeptide, inhibiting its transcription or translation, promoting the degradation of the mRNA, and inhibiting the expression of the polypeptide of the invention, thereby resulting in the inhibition of the polypeptide's function.
  • An antisense oligonucleotide derivative of the present invention can be made into an external preparation, such as a liniment or a poultice, by mixing with a suitable base material which is inactive against the derivatives.
  • the derivatives can be formulated into tablets, powders, granules, capsules, liposome capsules, injections, solutions, nose-drops, and freeze-dried agents by adding excipients, isotonic agents, solubilizers, stabilizers, preservatives, pain-killers, and such. These can be prepared following usual methods.
  • the antisense oligonucleotide derivative is given to the patient by directly applying onto the ailing site or by injecting into a blood vessel so that it will reach the site of ailment.
  • An antisense-mounting medium can also be used to increase durability and membrane-permeability. Examples are, liposome, poly-L-lysine, lipid, cholesterol, lipofectin, or derivatives of these.
  • the dosage of the antisense oligonucleotide derivative of the present invention can be adjusted suitably according to the patient's condition and used in desired amounts. For example, a dose range of 0.1 to 100 mg/kg, preferably 0.1 to 50 mg/kg can be administered.
  • the present invention also includes small interfering RNAs (siRNA) comprising a combination of a sense strand nucleic acid and an antisense strand nucleic acid of the nucleotide sequence of SEQ ID NO: 1, 3, or 5.
  • siRNA small interfering RNAs
  • siRNA refers to a double-stranded RNA molecule which prevents translation of a target mRNA. Standard techniques are used for introducing siRNA into cells, including those wherein DNA is used as the template to transcribe RNA.
  • the siRNA comprises a sense nucleic acid sequence and an antisense nucleic acid sequence of the polynucleotide encoding human CXADRL1, GCUD1, or RNF43 protein (SEQ ID NO: 1, 3, or 5).
  • the siRNA is constructed such that a single transcript (double-stranded RNA) has both the sense and complementary antisense sequences from a target gene, e.g., a hairpin.
  • the method is used to alter gene expression of a cell, i.e., up-regulate the expression of CXADRL1, GCUD1, or RNF43, e.g., as a result of malignant transformation of the cells. Binding of the siRNA to CXADRL1, GCUD1, or RNF43 transcript in the target cell results in a reduction of protein production by the cell.
  • the length of the oligonucleotide is at least 10 nucleotides and may be as long as the naturally occurring transcript.
  • the oligonucleotide is 19-25 nucleotides in length.
  • the oligonucleotide is less than 75, 50, or 25 nucleotides in length.
  • Examples of CXADRL1, GCUD1, or RNF43 siRNA oligonucleotides which inhibit the expression in mammalian cells include oligonucleotides containing any of SEQ ID NO: 112-114. These sequences are target sequence of the following siRNA sequences respectively.
  • the nucleotide sequence of siRNAs may be designed using an siRNA design computer program available from the Ambion website. Nucleotide sequences for the siRNA are selected byte computer program based on the following protocol:
  • the antisense oligonucleotide or siRNA of the invention inhibit the expression of the polypeptide of the invention and is thereby useful for suppressing the biological activity of the polypeptide of the invention.
  • expression-inhibitors comprising the antisense oligonucleotide or siRNA of the invention, are useful in the point that they can inhibit the biological activity of the polypeptide of the invention. Therefore, a composition comprising the antisense oligonucleotide or siRNA of the present invention is useful in treating a cell proliferative disease such as cancer.
  • the present invention provides a method for diagnosing a cell proliferative disease using the expression level of the polypeptides of the present invention as a diagnostic marker.
  • This diagnosing method comprises the steps of: (a) detecting the expression level of the CXADRL1, GCUD1, or RNF43 gene of the present invention; and (b) relating an elevation of the expression level to cell proliferative disease, such as cancer.
  • the expression levels of the CXADRL1, GCUD1, or RNF43 gene in a particular specimen can be estimated by quantifying mRNA corresponding to or protein encoded by the CXADRL1, GCUD1, or RNF43 gene. Quantification methods for mRNA are known to those skilled in the art. For example, the levels of mRNAs corresponding to the CXADRL1, GCUD1, or RNF43 gene can be estimated by Northern blotting or RT-PCR.
  • nucleotide sequences of the CXADRL1, GCUD1, or RNF43 genes are shown in SEQ ID NO: 1, 3, or 5, anyone skilled in the art can design the nucleotide sequences for probes or primers to quantify the CXADRL1, GCUD1, or RNF43 gene.
  • the expression level of the CXADRL1, GCUD1, or RNF43 gene can be analyzed based on the activity or quantity of protein encoded by the gene.
  • a method for determining the quantity of the CXADRL1, GCUD1, or RNF43 protein is shown below.
  • immunoassay method is useful for the determination of the proteins in biological materials. Any biological materials can be used for the determination of the protein or it's activity. For example, blood sample is analyzed for estimation of the protein encoded by a serum marker.
  • a suitable method can be selected for the determination of the activity of a protein encoded by the CXADRL1, GCUD1, or RNF43 gene according to the activity of each protein to be analyzed.
  • Expression levels of the CXADRL1, GCUD1, or RNF43 gene in a specimen are estimated and compared with those in a normal sample. When such a comparison shows that the expression level of the target gene is higher than those in the normal sample, the subject is judged to be affected with a cell proliferative disease.
  • the expression level of CXADRL1, GCUD1, or RNF43 gene in the specimens from the normal sample and subject may be determined at the same time. Alternatively, normal ranges of the expression levels can be determined by a statistical method based on the results obtained by analyzing the expression level of the gene in specimens previously collected from a control group.
  • the cell proliferative disease to be diagnosed is preferably cancer. More preferably, when the expression level of the CXADRL1, or GCUD1 gene is estimated and compared with those in a normal sample, the cell proliferative disease to be diagnosed is gastric, colorectal, or liver cancer; and when the RNF43 gene is estimated for its expression level, then the disease to be diagnosed is colorectal, lung, gastric, or liver cancer.
  • a diagnostic agent for diagnosing cell proliferative disease such as cancer including gastric, colorectal, lung, and liver cancers.
  • the diagnostic agent of the present invention comprises a compound that binds to a polynucleotide or a polypeptide of the present invention.
  • an oligonucleotide that hybridizes to the polynucleotide of the present invention, or an antibody that binds to the polypeptide of the present invention may be used as such a compound.
  • the present invention provides a method of screening for a compound for treating a cell proliferative disease using the polypeptide of the present invention.
  • An embodiment of this screening method comprises the steps of: (a) contacting a test compound with a polypeptide of the present invention, (b) detecting the binding activity between the polypeptide of the present invention and the test compound, and (c) selecting a compound that binds to the polypeptide of the present invention.
  • the polypeptide of the present invention to be used for screening may be a recombinant polypeptide or a protein derived from nature, or a partial peptide thereof.
  • Any test compound for example, cell extracts, cell culture supernatant, products of fermenting microorganism, extracts from marine organism, plant extracts, purified or crude proteins, peptides, non-peptide compounds, synthetic micromolecular compounds, and natural compounds, can be used.
  • the polypeptide of the present invention to be contacted with a test compound can be, for example, a purified polypeptide, a soluble protein, a form bound to a carrier, or a fusion protein fused with other polypeptides.
  • a method of screening for proteins for example, that bind to the polypeptide of the present invention using the polypeptide of the present invention
  • many methods well known by a person skilled in the art can be used.
  • Such a screening can be conducted by, for example, immunoprecipitation method, specifically, in the following manner.
  • the gene encoding the polypeptide of the present invention is expressed in animal cells and so on by inserting the gene to an expression vector for foreign genes, such as pSV2neo, pcDNA I, and pCD8.
  • the promoter to be used for the expression may be any promoter that can be used commonly and include, for example, the SV40 early promoter (Rigby in Williamson (ed.), Genetic Engineering, vol. 3.
  • the EF-1 ⁇ promoter (Kim et al., Gene 91: 217-23 (1990)), the CAG promoter (Niwa et al., Gene 108: 193-9 (1991)), the RSV LTR promoter (Cullen, Methods in Enzymology 152: 684-704 (1987)) the SR ⁇ promoter (Takebe et al., Mol Cell Biol 8: 466-72 (1988)), the CMV immediate early promoter (Seed and Aruffo, Proc Natl Acad Sci USA 84: 3365-9 (1987)), the SV40 late promoter (Gheysen and Fiers, J Mol Appl Genet 1: 385-94 (1982)), the Adenovirus late promoter (Kaufman et al., Mol Cell Biol 9: 946-58 (1989)), the HSV TK promoter, and so on.
  • the introduction of the gene into animal cells to express a foreign gene can be performed according to any methods, for example, the electroporation method (Chu et al., Nucleic Acids Res 15: 1311-26 (1987)), the calcium phosphate method (Chen and Okayama, Mol Cell Biol 7: 2745-52 (1987)), the DEAE dextran method (Lopata et al., Nucleic Acids Res 12: 5707-17 (1984); Sussman and Milman, Mol Cell Biol 4: 1641-3 (1984)), the Lipofectin method (Derijard, Cell 76: 1025-37 (1994); Lamb et al., Nature Genetics 5: 22-30 (1993): Rabindran et al., Science 259: 230-4 (1993)), and so on.
  • electroporation method Chou et al., Nucleic Acids Res 15: 1311-26 (1987)
  • the calcium phosphate method Choen and Okayama, Mol Cell Biol 7: 27
  • the polypeptide of the present invention can be expressed as a fusion protein comprising a recognition site (epitope) of a monoclonal antibody by introducing the epitope of the monoclonal antibody, whose specificity has been revealed, to the N- or C-terminus of the polypeptide of the present invention.
  • a commercially available epitope-antibody system can be used (Experimental Medicine 13: 85-90 (1995)).
  • Vectors which can express a fusion protein with, for example, ⁇ -galactosidase, maltose binding protein, glutathione S-transferase, green florescence protein (GFP), and so on by the use of its multiple cloning sites are commercially available.
  • a fusion protein prepared by introducing only small epitopes consisting of several to a dozen amino acids so as not to change the property of the polypeptide of the present invention by the fusion is also reported.
  • Epitopes such as polyhistidine (His-tag), influenza aggregate HA, human c-myc, FLAG, Vesicular stomatitis virus glycoprotein (VSV-GP), T7 gene 10 protein (T7-tag), human simple herpes virus glycoprotein (HSV-tag), E-tag (an epitope on monoclonal phage), and such, and monoclonal antibodies recognizing them can be used as the epitope-antibody system for screening proteins binding to the polypeptide of the present invention (Experimental Medicine 13: 85-90 (1995)).
  • an immune complex is formed by adding these antibodies to cell lysate prepared using an appropriate detergent.
  • the immune complex consists of the polypeptide of the present invention, a polypeptide comprising the binding ability with the polypeptide, and an antibody.
  • Immunoprecipitation can be also conducted using antibodies against the polypeptide of the present invention, besides using antibodies against the above epitopes, which antibodies can be prepared as described above.
  • an immune complex can be precipitated, for example by Protein A sepharose or Protein G sepharose when the antibody is a mouse IgG antibody.
  • an immune complex can be formed in the same manner as in the use of the antibody against the polypeptide of the present invention, using a substance specifically binding to these epitopes, such as glutathione-Sepharose 4B.
  • Immunoprecipitation can be performed by following or according to, for example, the methods in the literature (Harlow and Lane, Antibodies, 511-52, Cold Spring Harbor Laboratory publications, New York (1988)).
  • SDS-PAGE is commonly used for analysis of immunoprecipitated proteins and the bound protein can be analyzed by the molecular weight of the protein using gels with an appropriate concentration. Since the protein bound to the polypeptide of the present invention is difficult to detect by a common staining method, such as Coomassie staining or silver staining, the detection sensitivity for the protein can be improved by culturing cells in culture medium containing radioactive isotope, 35 S-methionine or 35 S-cystein, labeling proteins in the cells, and detecting the proteins. The target protein can be purified directly from the SDS-polyacrylamide gel and its sequence can be determined, when the molecular weight of a protein has been revealed.
  • a common staining method such as Coomassie staining or silver staining
  • a protein binding to the polypeptide of the present invention can be obtained by preparing a cDNA library from cells, tissues, organs (for example, tissues such as testis and ovary for screening proteins binding to CXADRL1; testis, ovary, and brain for screening proteins binding to GCUD1; and fetal lung, and fetal kidney for those binding to RNF43), or cultured cells expected to express a protein binding to the polypeptide of the present invention using a phage vector (e.g., ZAP), expressing the protein on LB-agarose, fixing the protein expressed on a filter, reacting the purified and labeled polypeptide of the present invention with the above filter, and detecting the plaques expressing proteins bound to the polypeptide of the present invention according to the
  • the polypeptide of the invention may be labeled by utilizing the binding between biotin and avidin, or by utilizing an antibody that specifically binds to the polypeptide of the present invention, or a peptide or polypeptide (for example, GST) that is fused to the polypeptide of the present invention. Methods using radioisotope, fluorescence, and such may be also used.
  • a two-hybrid system utilizing cells may be used (“MATCHMAKER Two-Hybrid system”, “Mammalian MATCHMAKER Two-Hybrid Assay Kit”, “MATCHMAKER one-Hybrid system” (Clontech); “HybriZAP Two-Hybrid Vector System” (Stratagene); the references “Dalton and Treisman, Cell 68: 597-612 (1992)”, “Fields and Sternglanz, Trends Genet 10: 286-92 (1994)”).
  • the polypeptide of the invention is fused to the SRF-binding region or GAL4-binding region and expressed in yeast cells.
  • a cDNA library is prepared from cells expected to express a protein binding to the polypeptide of the invention, such that the library, when expressed, is fused to the VP16 or GAL4 transcriptional activation region.
  • the cDNA library is then introduced into the above yeast cells and the cDNA derived from the library is isolated from the positive clones detected (when a protein binding to the polypeptide of the invention is expressed in yeast cells, the binding of the two activates a reporter gene, making positive clones detectable).
  • a protein encoded by the cDNA can be prepared by introducing the cDNA isolated above to E. coli and expressing the protein.
  • reporter gene for example, Ade2 gene, lacZ gene, CAT gene, luciferase gene, and such can be used in addition to the HIS3 gene.
  • a compound binding to the polypeptide of the present invention can also be screened using affinity chromatography.
  • the polypeptide of the invention may be immobilized on a carrier of an affinity column, and a test compound, containing a protein capable of binding to the polypeptide of the invention, is applied to the column.
  • a test compound herein may be, for example, cell extracts, cell lysates, etc. After loading the test compound, the column is washed, and compounds bound to the polypeptide of the invention can be prepared.
  • test compound When the test compound is a protein, the amino acid sequence of the obtained protein is analyzed, an oligo DNA is synthesized based on the sequence, and cDNA libraries are screened using the oligo DNA as a probe to obtain a DNA encoding the protein.
  • a biosensor using the surface plasmon resonance phenomenon may be used as a mean for detecting or quantifying the bound compound in the present invention.
  • a biosensor When such a biosensor is used, the interaction between the polypeptide of the invention and a test compound can-be observed real-time as a surface plasmon resonance signal, using only a minute amount of polypeptide and without labeling (for example, BIAcore, Pharmacia). Therefore, it is possible to evaluate the binding between the polypeptide of the invention and a test compound using a biosensor such as BIAcore.
  • the screening method of the present invention may comprise the following steps:
  • the reporter construct required for the screening can be prepared using the transcriptional regulatory region of a marker gene.
  • a reporter construct can be prepared based on the previous sequence information.
  • a nucleotide segment containing the transcriptional regulatory region can be isolated from a genome library based on the nucleotide sequence information of the marker gene.
  • a compound isolated by the screening is a candidate for drugs which promote or inhibit the activity of the polypeptide of the present invention, for treating or preventing diseases attributed to, for example, cell proliferative diseases, such as cancer.
  • the present invention provides methods for screening candidate agents which are potential targets in the treatment of cell proliferative disease.
  • candidate agents which are potential targets in the treatment of cell proliferative disease, can be identified through screenings that use the expression levels and activities of CXADRL1, GCUD1, or RNF43 as indices.
  • screening may comprise, for example, the following steps:
  • Cells expressing at least one of the CXADRL1, GCUD1, or RNF43 include, for example, cell lines established from gastric, colorectal, lung, or liver cancers; such cells can be used for the above screening of the present invention.
  • the expression level can be estimated by methods well known to one skilled in the art. In the method of screening, a compound that reduces the expression level of at least one of CXADRL1, GCUD1, or RNF43 can be selected as candidate agents.
  • the method utilizes biological activity of the polypeptide of the present invention as an index. Since the CXADRL1, GCUD1, and RNF43 proteins of the present invention have the activity of promoting cell proliferation, a compound which promotes or inhibits this activity of one of these proteins of the present invention can be screened using this activity as an index.
  • This screening method includes the steps of: (a) contacting a test compound with the polypeptide of the present invention; (b) detecting the biological activity of the polypeptide of step (a); and (c) selecting a compound that suppresses the biological activity of the polypeptide in comparison with the biological activity detected in the absence of the test compound.
  • Any polypeptides can be used for screening so long as they comprise the biological activity of the CXADRL1, GCUD1, or RNF43 protein.
  • biological activity includes cell-proliferating activity of the human CXADRL1, GCUD1, or RNF43 protein, and the activity of RNF43 to bind to NOTCH2 or STRIN.
  • a human CXADRL1, GCUD1, or RNF43 protein can be used and polypeptides functionally equivalent to these proteins can also be used.
  • Such polypeptides may be endogenously or exogenously expressed by cells.
  • test compounds for example, cell extracts, cell culture supernatants, products of fermenting microorganism, extracts of marine organism, plant extracts, purified or crude proteins, peptides, non-peptide compounds, synthetic micromolecular compounds, and natural compounds, can be used.
  • the compound isolated by this screening is a candidate for agonists or antagonists of the polypeptide of the present invention.
  • agonist refers to molecules that activate the function of the polypeptide of the present invention by binding thereto.
  • antagonist refers to molecules that inhibit the function of the polypeptide of the present invention by binding thereto.
  • a compound isolated by this screening is a candidate for compounds which inhibit the in vivo interaction of the polypeptide of the present invention with molecules (including DNAs and proteins).
  • the biological activity to be detected in the present method is cell proliferation
  • it can be detected, for example, by preparing cells which express the polypeptide of the present invention, culturing the cells in the presence of a test compound, and determining the speed of cell proliferation, measuring the cell cycle and such, as well as by measuring the colony forming activity as described in the Examples.
  • the compound isolated by the above screenings is a candidate for drugs which inhibit the activity of the polypeptide of the present invention and can be applied to the treatment of diseases associated with the polypeptide of the present invention, for example, cell proliferative diseases including cancer. More particularly, when the biological activity of CXADRL1 or GCUD1 protein is used as the index, compounds screened by the present method serve as a candidate for drugs for the treatment of gastric, colorectal, or liver cancer. On the other hand, when the biological activity of RNF43 protein is used as the index, compounds screened by the present method serve as a candidate for drugs for the treatment of colorectal, lung, gastric, or liver cancer.
  • the compound isolated by the above screenings is a polypeptide
  • a part of the structure of the compound inhibiting the activity of CXADRL1, GCUD1, or RNF43 protein is converted by addition, deletion, insertion, and/or replacement are also included in the compounds obtainable by the screening method of the present invention.
  • the method utilizes the binding ability of RNF43 to NOTCH2 or STRIN.
  • the RNF43 protein of the present invention was revealed to associated with NOTCH2 and STRIN.
  • the RNF43 protein of the present invention exerts the function of cell proliferation via its binding to molecules, such as NOTCH2 and STRIN.
  • the inhibition of the binding between the RNF43 protein and NOTCH2 or STRIN leads to the suppression of cell proliferation, and compounds inhibiting the binding serve as pharmaceuticals for treating cell proliferative disease such as cancer.
  • the cell proliferative disease treated by the compound screened by the present method is colorectal, lung, gastric, or liver cancer.
  • This screening method includes the steps of: (a) contacting a polypeptide of the present invention with NOTCH2 or STRIN in the presence of a test compound; (b) detecting the binding between the polypeptide and NOTCH2 or STRIN; and (c) selecting the compound that inhibits the binding between the polypeptide and NOTCH2 or STRIN.
  • the RNF43 polypeptide of the present invention, and NOTCH2 or STRIN to be used for the screening may be a recombinant polypeptide or a protein derived from nature, or may also be a partial peptide thereof so long as it retains the binding ability to each other.
  • the RNF43 polypeptide, NOTCH2 or STRIN to be used in the screening can be, for example, a purified polypeptide, a soluble protein, a form bound to a carrier, or a fusion protein fused with other polypeptides.
  • test compound for example, cell extracts, cell culture supernatants, products of fermenting microorganism, extracts from marine organism, plant extracts, purified or crude proteins, peptides, non-peptide compounds, synthetic micromolecular compounds, and natural compounds, can be used.
  • a method of screening for compounds that inhibit the binding between the RNF43 protein and NOTCH2 or STRIN many methods well known by one skilled in the art can be used. Such a screening can be carried out as an in vitro assay system, for example, in a cellular system. More specifically, first, either the RNF43 polypeptide, or NOTCH2 or STRIN is bound to a support, and the other protein is added together with a test sample thereto. Next, the mixture is incubated, washed, and the other protein bound to the support is detected and/or measured.
  • a compound interfering the association of CXADRL1 and AIP1 can be isolated by the present invention. It is expected that the inhibition of the binding between the CXADRL1 and AIP1 leads to the suppression of cell proliferation, and compounds inhibiting the binding serve as pharmaceuticals for treating cell proliferative disease such as cancer.
  • supports that may be used for binding proteins include insoluble polysaccharides, such as agarose, cellulose, and dextran; and synthetic resins, such as polyacrylamide, polystyrene, and silicon; preferably commercial available beads and plates (e.g., multi-well plates, biosensor chip, etc.) prepared from the above materials may be used. When using beads, they may be filled into a column.
  • insoluble polysaccharides such as agarose, cellulose, and dextran
  • synthetic resins such as polyacrylamide, polystyrene, and silicon
  • beads and plates e.g., multi-well plates, biosensor chip, etc.
  • binding of a protein to a support may be conducted according to routine methods, such as chemical bonding, and physical adsorption.
  • a protein may be bound to a support via antibodies specifically recognizing the protein.
  • binding of a protein to a support can be also conducted by means of avidin and biotin binding.
  • the binding between proteins is carried out in buffer, for example, but are not limited to, phosphate buffer and Tris buffer, as long as the buffer does not inhibit the binding between the proteins.
  • a biosensor using the surface plasmon resonance phenomenon may be used as a mean for detecting or quantifying the bound protein.
  • the interaction between the proteins can be observed real-time as a surface plasmon resonance signal, using only a minute amount of polypeptide and without labeling (for example, BIAcore, Pharmacia). Therefore, it is possible to evaluate the binding between the RNF43 polypeptide and NOTCH2 or STRIN using a biosensor such as BIAcore.
  • either the RNF43 polypeptide, or NOTCH2 or STRIN may be labeled, and the label of the bound protein may be used to detect or measure the bound protein. Specifically, after pre-labeling one of the proteins, the labeled protein is contacted with the other protein in the presence of a test compound, and then, bound proteins are detected or measured according to the label after washing.
  • Labeling substances such as radioisotope (e.g., 3 H, 14 C, 32 P, 33 P, 35 S, 125 I, 131 I), enzymes (e.g., alkaline phosphatase, horseradish peroxidase, ⁇ -galactosidase, ⁇ -glucosidase), fluorescent substances (e.g., fluorescein isothiosyanete (FITC), rhodamine), and biotin/avidin, may be used for the labeling of a protein in the present method.
  • radioisotope e.g., 3 H, 14 C, 32 P, 33 P, 35 S, 125 I, 131 I
  • enzymes e.g., alkaline phosphatase, horseradish peroxidase, ⁇ -galactosidase, ⁇ -glucosidase
  • fluorescent substances e.g., fluorescein isothiosyanete (FITC), r
  • proteins labeled with enzymes can be detected or measured by adding a substrate of the enzyme to detect the enzymatic change of the substrate, such as generation of color, with absorptiometer. Further, in case where a fluorescent substance is used as the label, the bound protein may be detected or measured using fluorophotometer.
  • the binding of the RNF43 polypeptide and NOTCH2 or STRIN can be also detected or measured using antibodies to the RNF43 polypeptide and NOTCH2 or STRIN.
  • the mixture is incubated and washed, and detection or measurement can be conducted using an antibody against NOTCH2 or STRIN.
  • NOTCH2 or STRIN may be immobilized on a support, and an antibody against RNF43 may be used as the antibody.
  • the antibody is preferably labeled with one of the labeling substances mentioned above, and detected or measured based on the labeling substance.
  • the antibody against the RNF43 polypeptide, NOTCH2, or STRIN may be used as a primary antibody to be detected with a secondary antibody that is labeled with a labeling substance.
  • the antibody bound to the protein in the screening of the present invention may be detected or measured using protein G or protein A column.
  • a two-hybrid system utilizing cells may be used (“MATCHMAKER Two-Hybrid system”, “Mammalian MATCHMAKER Two-Hybrid Assay Kit”, “MATCHMAKER one-Hybrid system” (Clontech); “HybriZAP Two-Hybrid Vector System” (Stratagene); the references “Dalton and Treisman, Cell 68: 597-612 (1992)”, “Fields and Sternglanz, Trends Genet 10: 286-92 (1994)”).
  • the RNF43 polypeptide of the invention is fused to the SRF-binding region or GAL4-binding region and expressed in yeast cells.
  • the NOTCH2 or STRIN binding to the RNF43 polypeptide of the invention is fused to the VP16 or GAL4 transcriptional activation region and also expressed in the yeast cells in the existence of a test compound.
  • the test compound does not inhibit the binding between the RNF43 polypeptide and NOTCH2 or STRIN, the binding of the two activates a reporter gene, making positive clones detectable.
  • reporter gene for example, Ade2 gene, lacZ gene, CAT gene, luciferase gene, and such can be used besides HIS3 gene.
  • the compound isolated by the screening is a candidate for drugs which inhibit the activity of the RNF43 protein of the present invention and can be applied to the treatment of diseases associated with the RNF43 protein, for example, cell proliferative diseases such as cancer, more particularly colorectal, lung, gastric, or liver cancer.
  • diseases associated with the RNF43 protein for example, cell proliferative diseases such as cancer, more particularly colorectal, lung, gastric, or liver cancer.
  • the compound isolated by the screening is a polypeptide, and a part of the structure of the compound inhibiting the binding between the RNF43 protein and NOTCH2 or STRIN is converted by addition, deletion, substitution, and/or insertion are also included in the compounds obtainable by the screening method of the present invention.
  • the isolated compound When administrating the compound isolated by the methods of the invention as a pharmaceutical for humans and other mammals, such as mice, rats, guinea-pigs, rabbits, chicken, cats, dogs, sheep, pigs, cattle, monkeys, baboons, and chimpanzees, for treating a cell proliferative disease (e.g., cancer) the isolated compound can be directly administered or can be formulated into a dosage form using known pharmaceutical preparation methods.
  • the drugs can be taken orally, as sugarcoated tablets, capsules, elixirs and microcapsules, or non-orally, in the form of injections of sterile solutions or suspensions with water or any other pharmaceutically acceptable liquid.
  • the compounds can be mixed with pharmacologically acceptable carriers or medium, specifically, sterilized water, physiological saline, plant-oil, emulsifiers, suspending agents, surfactants, stabilizers, flavoring agents, excipients, vehicles, preservatives, binders, and such, in a unit dose form required for generally accepted drug implementation.
  • pharmacologically acceptable carriers or medium specifically, sterilized water, physiological saline, plant-oil, emulsifiers, suspending agents, surfactants, stabilizers, flavoring agents, excipients, vehicles, preservatives, binders, and such, in a unit dose form required for generally accepted drug implementation.
  • the amount of active ingredients in these preparations makes a suitable dosage within the indicated range acquirable.
  • additives that can be mixed to tablets and capsules are, binders such as gelatin, corn starch, tragacanth gum, and arabic gum; excipients such as crystalline cellulose; swelling agents such as corn starch, gelatin, and alginic acid; lubricants such as magnesium stearate; sweeteners such as sucrose, lactose, and saccharin; flavoring agents such as peppermint, Gaultheria adenothrix oil, and cherry.
  • a liquid carrier such as oil, can also be further included in the above ingredients.
  • Sterile composites for injections can be formulated following normal drug implementations using vehicles such as distilled water used for injections.
  • Physiological saline, glucose, and other isotonic liquids including adjuvants can be used as aqueous solutions for injections.
  • adjuvants such as D-sorbitol, D-mannnose, D-mannitol, and sodium chloride
  • Suitable solubilizers such as alcohol, specifically ethanol; polyalcohols, such as propylene glycol and polyethylene glycol; and non-ionic surfactants, such as Polysorbate 80 (TM) and HCO-50.
  • Sesame oil or Soy-bean oil can be used as a oleaginous liquid and may be used in conjunction with benzyl benzoate or benzyl alcohol as a solubilizer and may be formulated with a buffer, such as phosphate buffer and sodium acetate buffer; a pain-killer, such as procaine hydrochloride; a stabilizer, such as benzyl alcohol, phenol; and an anti-oxidant.
  • the prepared injection may be filled into a suitable ampule.
  • Methods well known to one skilled in the art may be used to administer the inventive pharmaceutical compound to patients, for example as intraarterial, intravenous, percutaneous injections, and also as intranasal, transbronchial, intramuscular, or oral administrations.
  • the dosage and method of administration vary according to the body-weight and age of a patient and the administration method; however, one skilled in the art can routinely select them. If said compound is encodable by a DNA, the DNA can be inserted into a vector for gene therapy and the vector administered to perform the therapy.
  • the dosage and method of administration vary according to the body-weight, age, and symptoms of a patient but one skilled in the art can select them suitably.
  • the dose of a compound that binds with the polypeptide of the present invention and regulates its activity is about 0.1 mg to about 100 mg per day, preferably about 1.0 mg to about 50 mg per day and more preferably about 1.0 mg to about 20 mg per day, when administered orally to a normal adult (weight 60 kg).
  • the present invention provides a method for treating or preventing a cell proliferative disease, such as cancer, using an antibody against the polypeptide of the present invention.
  • a pharmaceutically effective amount of an antibody against the polypeptide of the present invention is administered. Since the expression of the CXADRL1, GCUD1, and RNF43 protein are up-regulated in cancer cells, and the suppression of the expression of these proteins leads to the decrease in cell proliferating activity, it is expected that cell proliferative diseases can be treated or prevented by binding the antibody and these proteins.
  • an antibody against the polypeptide of the present invention are administered at a dosage sufficient to reduce the activity of the protein of the present invention, which is in the range of 0.1 to about 250 mg/kg per day.
  • the dose range for adult humans is generally from about 5 mg to about 17.5 g/day, preferably about 5 mg to about 10 g/day, and most preferably about 100 mg to about 3 g/day.
  • an antibody binding to a cell surface marker specific for tumor cells can be used as a tool for drug delivery.
  • the antibody conjugated with a cytotoxic agent is administered at a dosage sufficient to injure tumor cells.
  • the present invention also relates to a method of inducing anti-tumor immunity comprising the step of administering CXADRL1, GCUD1, or RNF43 protein, an immunologically active fragment thereof, or a polynucleotide encoding the protein or fragments thereof.
  • the CXADRL1, GCUD1, or RNF43 protein, or the immunologically active fragments thereof are useful as vaccines against cell proliferative diseases.
  • the proteins or fragments thereof may be administered in a form bound to the T cell receptor (TCR) or presented by an antigen presenting cell (APC), such as macrophage, dendritic cell (DC), or B-cells. Due to the strong antigen presenting ability of DC, the use of DC is most preferable among the APCs.
  • vaccine against cell proliferative disease refers to a substance that has the function to induce anti-tumor immunity upon inoculation into animals.
  • polypeptides comprising the amino acid sequence of SEQ ID NO: 80, 97, or 108 were suggested to be HLA-A24 or HLA-A*0201 restricted epitope peptides that may induce potent and specific immune response against colorectal, lung, gastric, or liver cancer cells expressing RNF43.
  • polypeptides comprising the amino acid sequence of SEQ ID NO:124 was suggested to be HLA-A*0201 restricted epitopes peptides that may induce potent and specific immune response against colorectal, gastric, or liver cancer cells expressing CXADRL1.
  • polypeptides comprising the amino acid sequence of SEQ ID NO: 164 was suggested to be HLA-A*0201 restricted epitopes peptides that may induce potent and specific immune response against colorectal, gastric, or liver cancer cells expressing GCUD1.
  • the present invention also encompasses method of inducing anti-tumor immunity using polypeptides comprising the amino acid sequence of SEQ ID NO: 80, 97, 108, 124 or 164.
  • anchor residue(s) refers to amino acid residues of the epitope that binds to the HLA class I peptide-binding cleft, but that does not contact with TCR; more specifically, positions two and nine of an epitope peptide is considered to be such anchor residues. According to the HLA-A2 antigen motif previously reported by Smith et al.
  • nonamer peptides wherein the amino acid at position two is Leu or Ile, or the amino acid at position nine is Leu, Ile, or Val are preferred examples as the polypeptide to be administered according to the present invention.
  • Particularly preferable examples of such nonamer peptides include those having the amino acid sequence of SEQ ID NOs: 195-198.
  • the present invention is not restricted to these examples and any modification may be introduced into the polypeptides used for the present invention.
  • anti-tumor immunity includes immune responses such as follows:
  • the protein when a certain protein induces any one of these immune responses upon inoculation into an animal, the protein is decided to have anti-tumor immunity inducing effect.
  • the induction of the anti-tumor immunity by a protein can be detected by observing in vivo or in vitro the response of the immune system in the host against the protein.
  • cytotoxic T lymphocytes For example, a method for detecting the induction of cytotoxic T lymphocytes is well known.
  • a foreign substance that enters the living body is presented to T cells and B cells by the action of antigen presenting cells (APCs).
  • APCs antigen presenting cells
  • T cells that respond to the antigen presented by APC in antigen specific manner differentiate into cytotoxic T cells (or cytotoxic T lymphocytes; CTLs) due to stimulation by the antigen, and then proliferate (this is referred to as activation of T cells). Therefore, CTL induction by a certain peptide can be evaluated by presenting the peptide to T cell by APC, and detecting the induction of CTL.
  • APC has the effect of activating CD4+ T cells, CD8+ T cells, macrophages, eosinophils, and NK cells. Since CD4+ T cells and CD8+ T cells are also important in anti-tumor immunity, the anti-tumor immunity inducing action of the peptide can be evaluated using the activation effect of these cells as indicators.
  • a method for evaluating the inducing action of CTL using dendritic cells (DCs) as APC is well known in the art.
  • DC is a representative APC having the strongest CTL inducing action among APCs.
  • the test polypeptide is initially contacted with DC, and then this DC is contacted with T cells. Detection of T cells having cytotoxic effects against the cells of interest after the contact with DC shows that the test polypeptide has an activity of inducing cytotoxic T cells.
  • Activity of CTL against tumors can be detected, for example, using the lysis of 51 Cr-labeled tumor cells as the indicator.
  • the method of evaluating the degree of tumor cell damage using 3 H-thymidine uptake activity or LDH (lactose dehydrogenase)-release as the indicator is also well known.
  • peripheral blood mononuclear cells may also be used as the APC.
  • the induction of CTL is reported that it can be enhanced by culturing PBMC in the presence of GM-CSF and IL-4.
  • CTL has been shown to be induced by culturing PBMC in the presence of keyhole limpet hemocyanin (KLH) and IL-7.
  • KLH keyhole limpet hemocyanin
  • test polypeptides confirmed to possess CTL inducing activity by these methods are polypeptides having DC activation effect and subsequent CTL inducing activity. Therefore, polypeptides that induce CTL against tumor cells are useful as vaccines against tumors. Furthermore, APC that acquired the ability to induce CTL against tumors by contacting with the polypeptides are useful as vaccines against tumors. Furthermore, CTL that acquired cytotoxicity due to presentation of the polypeptide antigens by APC can be also used as vaccines against tumors. Such therapeutic methods for tumors using anti-tumor immunity due to APC and CTL are referred to as cellular immunotherapy.
  • the induction of anti-tumor immunity by a polypeptide can be confirmed by observing the induction of antibody production against tumors. For example, when antibodies against a polypeptide are induced in a laboratory animal immunized with the polypeptide, and when growth of tumor cells is suppressed by those antibodies, the polypeptide can be determined to have an ability to induce anti-tumor immunity.
  • Anti-tumor immunity is induced by administering the vaccine of this invention, and the induction of anti-tumor immunity enables treatment and prevention of cell proliferating diseases, such as gastric, colorectal, lung, and liver cancers.
  • Therapy against cancer or prevention of the onset of cancer includes any of the steps, such as inhibition of the growth of cancerous cells, involution of cancer, and suppression of occurrence of cancer. Decrease in mortality of individuals having cancer, decrease of tumor markers in the blood, alleviation of detectable symptoms accompanying cancer, and such are also included in the therapy or prevention of cancer. Such therapeutic and preventive effects are preferably statistically significant.
  • the above-mentioned protein having immunological activity or a vector encoding the protein may be combined with an adjuvant.
  • An adjuvant refers to a compound that enhances the immune response against the protein when administered together (or successively) with the protein having immunological activity.
  • adjuvants include cholera toxin, salmonella toxin, alum, and such, but are not limited thereto.
  • the vaccine of this invention may be combined appropriately with a pharmaceutically acceptable carrier. Examples of such carriers are sterilized water, physiological saline, phosphate buffer, culture fluid, and such.
  • the vaccine may contain as necessary, stabilizers, suspensions, preservatives, surfactants, and such.
  • the vaccine is administered systemically or locally. Vaccine administration may be performed by single administration, or boosted by multiple administrations.
  • tumors can be treated or prevented, for example, by the ex vivo method. More specifically, PBMCs of the subject receiving treatment or prevention are collected, the cells are contacted with the polypeptide ex vivo, and following the induction of APC or CTL, the cells may be administered to the subject.
  • APC can be also induced by introducing a vector encoding the polypeptide into PBMCs ex vivo.
  • APC or CTL induced in vitro can be cloned prior to administration. By cloning and growing cells having high activity of damaging target cells, cellular immunotherapy can be performed more effectively.
  • APC and CTL isolated in this manner may be used for cellular immunotherapy not only against individuals from whom the cells are derived, but also against similar types of tumors from other individuals.
  • a pharmaceutical composition for treating or preventing a cell proliferative disease, such as cancer comprising a pharmaceutically effective amount of the polypeptide of the present invention.
  • the pharmaceutical composition may be used for raising anti-tumor immunity.
  • CXADRL1 restricted to testis and ovary
  • GCUD1 normal expression of GCUD1
  • RNF43 normal expression of RNF43
  • the CXADRL1 and GCUD1 polypeptides are preferable for treating cell proliferative disease, especially gastric, colorectal, or liver cancer; and RNF43 polypeptide is preferable for treating cell proliferative disease, especially colorectal, lung, gastric, and liver cancers.
  • polypeptides comprising the amino acid sequence of SEQ ID NO: 80, 97, or 108 are preferable examples of polypeptides that can be used in a pharmaceutical composition for treating or preventing cell proliferative disease, especially colorectal, lung, gastric, and liver cancers.
  • polypeptide comprising the amino acid sequence of SEQ ID NO: 124 is a preferable example of polypeptide that can be used in a pharmaceutical composition for treating or preventing cell proliferative disease, especially colorectal, lung, gastric, and liver cancers.
  • anchor-modified polypeptides of the polypeptide comprising the amino acid sequence of SEQ ID NO: 124 were revealed to exhibit increased binding affinity to HLA-A*0201 molecules, activate a certain portion of TCR repertoire recognizing the naturally processed wild-type epitope peptide presented by tumor cells, and elicit native peptide specific CTSs more frequently and abundantly than the wild-type peptide.
  • anchor-modified polypeptides are preferable examples of polypeptide that can be used in a pharmaceutical composition for treating or preventing the cell proliferative diseases.
  • Example of these anchor-modified polypeptides includes those having the amino acid sequences of SEQ ID NOs: 195 and 196.
  • polypeptide comprising the amino acid sequence of SEQ ID NO: 164 is a preferable example of polypeptide that can be used in a pharmaceutical composition for treating or preventing cell proliferative disease, especially colorectal, lung, gastric, and liver cancers.
  • anchor-modified polypeptide of the polypeptides comprising the amino acid sequence of SEQ ID NO: 164 were revealed to exhibit increased binding affinity to HLA-A*0201 molecules, activate a certain portion of TCR repertoire recognizing the naturally processed wild-type epitope peptide presented by tumor cells, and elicit native peptide specific CTSs more frequently and abundantly than the wild-type peptide.
  • anchor-modified polypeptides are preferable examples of polypeptide that can be used in a pharmaceutical composition for treating or preventing the cell proliferative diseases.
  • Example of these anchor-modified polypeptides includes those having the amino acid sequences of SEQ ID NOs: 197 and 198.
  • the polypeptide or fragment thereof is administered at a dosage sufficient to induce anti-tumor immunity, which is in the range of 0.1 mg to 10 mg, preferably 0.3 mg to 5 mg, more preferably 0.8 mg to 1.5 mg.
  • the administrations are repeated.
  • 1 mg of the peptide or fragment thereof may be administered 4 times in every two weeks for inducing the anti-tumor immunity.
  • RNA extracted from microdissected tissue was amplified with Ampliscribe T7 Transcription Kit (Epicentre Technologies) and labeled during reverse transcription with Cy-dye (Amersham) (RNA from non-cancerous tissue with Cy5 and RNA from tumor with Cy3). Hybridization, washing, and detection were carried out as described previously (Ono et al., Cancer Res. 60: 5007-11 (2000)), and fluorescence intensity of Cy5 and Cy3 for each target spot was measured using Array Vision software (Amersham Pharmacia). After subtraction of background signal, duplicate values were averaged for each spot.
  • Human embryonic kidney 293 (HEK293) were obtained from TaKaRa. COS7 cell, NIH3T3 cell, human cervical cancer cell line HeLa, human gastric cancer cell lines MKN-1 and MKN-28, human hepatoma cell line Alexander, and human colon cancer cell lines, LoVo, HCT116, DLD-1 and SW480, were obtained from the American Type Culture Collection (ATCC, Rockville, Md.). Human hepatoma cell line SNU475 and human colon cancer cell lines, SNUC4 and SNUC5, were obtained from the Korea cell-line bank.
  • All cells were grown in monolayers in appropriate media: Dulbecco's modified Eagle's medium for COS7, NIH3T3, HEK293, and Alexander; RPMI1640 for MKN-1, MKN-28, SNU475, SNUC4, DLD-1 and SNUC5; McCoy's 5A medium for HCT116; Leibovitz's L-15 for SW480; HAM's F-12 for LoVo; and Eagle's minimum essential medium for HeLa (Life Technologies, Grand Island, N.Y.). All media were supplemented with 10% fetal bovine serum and 1% antibiotic/antimycotic solution (Sigma). A human gastric cancer cell line St-4 was kindly provided by Dr. Tsuruo of Cancer Institute in Japan.
  • St-4 cells were grown in monolayers in RPMI1640 supplemented with 10% fetal bovine serum and 1% antibiotic/antimycotic solution (Sigma).
  • T2 cells HLA-A*0201
  • EHM HLA-A3/3
  • human B-lymphoblastoid cell lines were generous gifts from Prof. Shiku (Univ. Mie).
  • HT29 colon carcinoma cell line; HLA-A24/01
  • WiDR colon carcinoma cell line; HLA-A24/01
  • HCT116 colon carcinoma cell line; HLA-A02/01
  • DLD-1 colon carcinoma cell line; HLA-A24/01
  • SNU475 hepatocellular carcinoma cell line; HLA-A*0201
  • MKN45 gastric cancer cell line; HLA-A2 negative
  • MKN74 gastric cancer cell line; HLA-A2 negative
  • TISI cells HLA-A24/24) were generous gifts from Takara Shuzo Co, Ltd. (Otsu, Japan).
  • RT-PCR examinations revealed strong CXADRL1 expression in SNU475 and MKN74, and strong GCUD1 expression in SNU475 and MKN45.
  • Amplification was conducted under following conditions: denaturing for 4 min at 94° C., followed by 20 (for GAPDH), 35 (for CXADRL1), 30 (for GCUD1), 30 (for RNF43) cycles of 94° C. for 30 s, 56° C. for 30 s, and 72° C. for 45 s, in GeneAmp PCR system 9700 (Perkin-Elmer, Foster City, Calif.).
  • Primer sequences were; for GAPDH: forward, 5′-ACAACAGCCTCAAGATCATCAG (SEQ ID NO: 7) and reverse, 5′-GGTCCACCACTGACACGTTG (SEQ ID NO: 8); for CXADRL1: forward, 5′-AGCTGAGACATTTGTTCTCTTG (SEQ ID NO: 9) and reverse: 5′-TATAAACCAG CTGAGTCCAGAG (SEQ ID NO: 10); for GCUD1 forward: 5′-TTCCCGATATCAACATCTACCAG (SEQ ID NO: 11) reverse: 5′-AGTGTGTGACCTCAATAAGGCAT (SEQ ID NO: 12), for RNF43 forward; 5′-CAGGCTTTGGACGCACAGGACTGGTAC-3′ (SEQ ID NO: 13) and reverse; 5′-CTTTGTGATCATCCTGGCTTCGGTGCT-3′ (SEQ ID NO: 14).
  • Human multiple-tissue blots (Clontech, Palo Alto, Calif.) were hybridized with 32 P-labeled PCR products of CXADRL1, GCUD1, or RNF43. Pre-hybridization, hybridization and washing were performed according to the supplier's recommendations. The blots were autoradiographed with intensifying screens at ⁇ 80° C. for 24 to 72 h.
  • 5′ RACE experiments were carried out using Marathon cDNA amplification kit (Clontech) according to the manufacturer's instructions.
  • CXADRL1 Marathon cDNA amplification kit
  • gene-specific reverse primers 5′-GGTTGAGATTTAAGTTCTCAAA-3′ (SEQ ID NO: 15)
  • AP-1 primer supplied with the kit were used.
  • the cDNA template was synthesized from human testis mRNA (Clontech).
  • the PCR products were cloned using TA cloning kit (Invitrogen) and their sequences were determined with ABI PRISM 3700 DNA sequencer (Applied Biosystems).
  • CXADRL1, GCUD1, and RNF43 were amplified by RT-PCR using gene specific primer sets; for CXADRL1, 5′-AGTTAAGCTTGCCGGGATGACTTCTCAGCGTTCCCCTCTGG-3′ (SEQ ID NO: 16) and 5′-ATCTCGAGTACCAAGGACCCGGCCCGACTCTG-3′ (SEQ ID NO: 17); for GCUD15′-GCGGATCCAGGATGGCTGCTGCAGCTCCTCCAAG-3′ (SEQ ID NO: 18) and 5′-TAGAATTCTTAAAGAACTTAATCTCCGTGTCAACAC-3′ (SEQ ID NO: 19); and for RNF43, 5′-TGCAGATCTGCAGCTGGTAGCATGAGTGGTG-3′ (SEQ ID NO: 20) and 5′-GAGGAGCTGTGTGAACAGGCTGTGTGAGATGT-3′ (SEQ ID NO: 21).
  • the PCR products were cloned into appropriate cloning site of either pc
  • Cells transfected with pcDNA3.1 myc/His-CXADRL1, pcDNA3.1 myc/His-GCUD1, pcDNA3.1 myc/His-RNF43, or pcDNA3.1 myc/His-LacZ were washed twice with PBS and harvested in lysis buffer (150 mM NaCl, 1% Triton X-100, 50 mM Tris-HCl pH 7.4, 1 mM DTT, and 1 ⁇ complete Protease Inhibitor Cocktail (Boehringer)). Following homogenization, the cells were centrifuged at 10,000 ⁇ g for 30 min, the supernatant were standardized for protein concentration by the Bradford assay (Bio-Rad).
  • lysis buffer 150 mM NaCl, 1% Triton X-100, 50 mM Tris-HCl pH 7.4, 1 mM DTT, and 1 ⁇ complete Protease Inhibitor Cocktail (Boehringer)
  • Proteins were separated by 10% SDS-PAGE and immunoblotted with mouse anti-myc (SANTA CRUZ) antibody.
  • HRP-conjugated goat anti-mouse IgG (Amersham) served as the secondary antibody for the ECL Detection System (Amersham).
  • Cells transfected with pcDNA3.1 myc/His-CXADRL1, pcDNA3.1 myc/His-GCUD1, pcDNA3.1 myc/His-RNF43, or pcDNA3.1 myc/His-LacZ were fixed with PBS containing 4% paraformaldehyde for 15 min, then made permeable with PBS containing 0.1% Triton X-100 for 2.5 min at RT. Subsequently the cells were covered with 2% BSA in PBS for 24 h at 4° C. to block non-specific hybridization.
  • Mouse anti-myc monoclonal antibody (Sigma) at 1:1000 dilution was used as the primary antibody, and the reaction was visualized after incubation with Rhodamine-conjugated anti-mouse secondary antibody (Leinco and ICN). Nuclei were counter-stained with 4′,6′-diamidine-2′-phenylindole dihydrochloride (DAPI). Fluorescent images were obtained under an ECLIPSE E800 microscope.
  • Cells plated at a density of 5 ⁇ 10 5 cells/100 mm dish were transfected in triplicate with sense or antisense S-oligonucleotides designated to suppress the expression of CXADRL1, GCUD1, or RNF43. Seventy-two hours after transfection, the medium was replaced with fresh medium containing 500 ⁇ g/ml of MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) (Sigma) and the plates were incubated for four hours at 37° C.
  • MTT 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide
  • the cells were lysed by the addition of 1 ml of 0.01 N HCl/10% SDS and the absorbance of lysates was measured with ELISA plate reader at a test wavelength of 570 nm (reference, 630 nm).
  • the cell viability was represented by the absorbance compared to that of control cells.
  • H1RNA gene was reported to be transcribed by RNA polymerase III, which produce short transcripts with uridines at the 3′ end
  • a genomic fragment of HI RNA gene containing its promoter region was amplified by PCR using a set of primers [5′-TGGTAGCCAAGTGCAGGTTATA-3′ (SEQ ID NO: 32), and 5′-CCAAAGGGTTTCTGCAGTTTCA-3′ (SEQ ID NO: 33)] and human placental DNA as a template.
  • the products were purified and cloned into pCR2.0 plasmid vector using TA cloning kit (Invitrogen) according to the supplier's protocol.
  • the BamHI and XhoI fragment containing the H1RNA gene was purified and cloned into pcDNA3.1(+) plasmid at the nucleotide position from 1257 to 56, which plasmid was amplified by PCR with a set of primers, 5′-TGCGGATCCAGAGCAGATTGTACTGAGAGT-3′ (SEQ ID NO: 34) and 5′-CTCTATCTCGAGTGAGGCGGAAAGAACCA-3′ (SEQ ID NO: 35), and then digested with BamHI and XhoI.
  • the ligated DNA was used as a template for PCR with primers, 5′-TTTAAGCTTGAAGACCATTTTTGGAAAAAAAAAAAAAAAAAAAAC-3′ (SEQ ID NO: 36) and 5′-TTTAAGCTTGAAGACATGGGAAAGAGTGGTCA-3′ (SEQ ID NO: 37).
  • the product was digested with HindIII, and subsequently self-ligated to produce psiH1BX3.0 vector plasmid.
  • psiH1BX-EGFP was prepared by cloning double-stranded oligonucleotides of 5′-CACCGAAGCAGCACGACTTCTTCTTCAAGAGAGAAGAAGTCGTGCTGCTTC -3′ (SEQ ID NO: 38) and 5′-AAAAGAAGCAGCACGACTTCTTCTCTCTTGAAGAAGAAGTCGTGCTGCTTC -3′ (SEQ ID NO: 39) into the BbsI site of the psiH1BX vector.
  • a plasmid expressing either RNF43-siRNA or CXADRL1-siRNA was prepared by cloning double-stranded oligonucleotides into psiH1BX3.0 vector. Oligonucleotides used as RNF43 siRNAs were:
  • the amino- and carboxyl-terminal regions of RNF43 was amplified by RT-PCR using following sets of primers: 5′-GAAGATCTGCAGCGGTGGAGTCTGAAAG-3′ (SEQ ID NO: 64) and 5′-GGAATTCGGACTGGGAAAATGAATCTCCCTC-3′ (SEQ ID NO: 65) for the amino-terminal region; and 5′-GGAGATCTCCTGATCAGCAAGTCACC-3′ (SEQ ID NO: 66) and 5′-GGAATTCCACAGCCTGTTCACACAGCTCCTC-3′ (SEQ ID NO: 67) for the carboxyl-terminal region.
  • the products were digested with BamHI-EcoRI and cloned into the BamHI-EcoRI site of pET-43.1a (+) vector (Novagen).
  • the plasmids were transfected into E. coli BL21trxB(DE3)pLysS cells (Stratagene). Recombinant RNF43 protein was extracted from cells cultured at 25° C. for 16 h after the addition of 0.2 mM IPTG.
  • Yeast two-hybrid assay was performed using MATCHMAKER GAL4 Two-Hybrid System 3 (Clontech) according to the manufacturer's protocols.
  • the entire coding sequence of RNF43 was cloned into the EcoR I-BamH I site of pAS2-1 vector as a bait for screening human-testis cDNA library (Clontech).
  • pAS2-RNF43 was used as bait vector, pACT2-NOTCH2 and pACT2-STRIN as prey vector.
  • CXADRL1 was cloned into the EcoRI site of pAS2-1 vector as a bait for screening human testis cDNA library (Clontech). To confirm interaction in yeast, pAS2-CXADRL1 was used as the bait vector, and pACT2-AIP1 as the prey vector. (18) Preparation of CXADRL Specific Antibody
  • Anti-CXADRL antisera were prepared by immunization with synthetic polypeptides of CXADRL1 encompassing codons from 235 to 276 for Ab-1, from 493 to 537 for Ab-2, or from 70 to 111 for Ab-3. Sera were purified using recombinant His-tagged CXADRL1 protein prepared in E. coli transfected with pET-CXADRL plasmid. Protein extracted from cells expressing Flag-tagged CXADRL1 was further separated by 10% SDS-PAGE and immunoblotted with either anti-CXADRL1 sera or anti-Flag antibody.
  • HRP-conjugated goat anti-rabbit IgG or HRP-conjugated sheep anti-mouse IgG antibody served as the secondary antibody, respectively, for ECL Detection System (Amersham Pharmacia Biotech, Piscataway, N.J.). Immunoblotting with anti-CXADRL antisera showed a 50 kD band of FLAG-tagged CXADRL1, which pattern was identical to that detected with anti-FLAG antibody.
  • recombinant GCUD1 protein was prepared.
  • the entire coding region of GCUD1 was amplified by RT-PCR with a set of primers, 5′-GCGGATCCAGGATGGCTGCAGCTCCTCCAAG-3′ (SEQ ID NO: 68) and 5′-CTGAATTCACTTAAAGAACTTAATCTCCGTGTCAACAC-3′ (SEQ ID NO: 69).
  • the product was purified, digested with BamH1 and EcoR1, and cloned into an appropriate cloning site of pGEX6P-2.
  • the resulting plasmid was dubbed pGEX-GCUD1.
  • pGEX-GCUD1 plasmid was transformed into E. coli DH10B.
  • the production of the recombinant protein was induced by the addition of IPTG, and the protein was purified with Glutathione SepharoseTM 4B (Amersham Pharmacia) according to the manufacturers' protocols.
  • Polyclonal antibody against GCUD1 was purified from the serum. Proteins from cells transfected with plasmids expressing Flag-tagged GCUD1 were separated by 10% SDS-PAGE and immunoblotted with anti-GCUD1 or anti-Flag antibody. HRP-conjugated goat anti-rabbit IgG (Santa Cruz Biotechnology, Santa Cruz, Calif.) or HRP-conjugated anti-Flag antibody served as the secondary antibody, respectively, for ECL Detection System (Amersham Pharmacia Biotech, Piscataway, N.J.). Immunoblotting with the anti-GCUD1 antibody showed a 47 kD band of FLAG-tagged GCUD1, which pattern was identical to that detected with the anti-FLAG antibody.
  • DCs Monocyte-derived dendritic cells
  • APCs antigen-presenting cells
  • DCs were generated in vitro as described elsewhere (Nukaya et al., Int J Cancer 80: 92-7 (1999); Tsai et al., J Immunol 158: 1796-802 (1997)).
  • PBMCs peripheral blood mononuclear cells
  • monocyte fraction of PBMCs were separated by adherence to a plastic tissue culture flask (Becton Dickinson).
  • This monocyte fraction was cultured for seven days in AIM-V medium (Invitrogen) containing 2% heat-inactivated autologous serum (AS), 1000 U/ml of GM-CSF (provided by Kirin Brewery Company), and 1000 U/ml of IL-4 (Genzyme) to obtain DCs fraction.
  • AIM-V medium Invitrogen
  • AS heat-inactivated autologous serum
  • GM-CSF GM-CSF
  • IL-4 Gene
  • peptide-pulsed antigen presenting cells were then irradiated (5500 rad) and mixed at a 1:20 ratio with autologous CD8+ T cells, obtained by positive selection with Dynabeads M-450 CD8 (Dynal) and Detachabead (Dynal). These cultures were set up in 48-well plates (Corning); each well contained 1.5 ⁇ 10 4 peptide-pulsed antigen presenting cells, 3 ⁇ 10 5 CD8+ T cells and 10 ng/ml of IL-7 (Genzyme) in 0.5 ml of AIM-V with 2% AS. Three days later, these cultures were supplemented with IL-2 (CHIRON) to a final concentration of 20 IU/ml.
  • IL-2 CHIRON
  • the T cells were further restimulated with the autologous peptide-pulsed antigen presenting cells which were prepared each time in the same manner as described above. Lymphoid cells in the culture on day 21 were harvested and tested for cytotoxicity against peptide-pulsed TISI or T2 cells.
  • lymphoid cells with proved significant cytotoxicity against peptide-pulsed TISI or T2 were further expanded in culture using a method similar to that described by Riddell, et al. (Walter et al., N Engl J Med 333:1038-1044, 1995; Riddell et al., Nature Med. 2:216-23 (1996)).
  • 5 ⁇ 10 4 of lymphoid cells were resuspended in 25 ml of AIM-V supplemented with 5% AS containing 25 ⁇ 10 6 irradiated (3300 rads) PBMC, 5 ⁇ 10 6 irradiated (8000 rads) EHM cells, and 40 ng/ml of anti-CD3 monoclonal antibody (Pharmingen).
  • 120 IU/ml of IL-2 were added to the cultures.
  • the cultures comprised fresh AIM-V supplemented with 5% AS and 30 IU/ml of IL-2 on days 5, 8 and 11.
  • CTL clones Some of the lymphoid cells with potent cytotoxicity were used to obtain CTL clones.
  • the cell suspensions were diluted to densities of 0.3, 1, and 3 CTLs/lymphoid cells per well in 96 round-bottom microtiter plate (Nalge Nunc International). These cells were cultured in 150 ⁇ l/well of AIM-V supplemented with 5% AS containing 7 ⁇ 10 4 cells/well of allogenic PBMCs, 1 ⁇ 10 4 cells/well of EHM, 30 ng/ml of anti-CD3 antibody, and 125 U/ml of IL-2. 10 days later, 50 ⁇ l/well of IL-2 was added to the medium to a final concentration of 125 U/ml. Cytotoxic activity of cultured CTLs was tested on day 14, and CTL clones were expanded using the same method as described above.
  • Target cells were labeled with 100 ⁇ Ci of Na 2 51 CrO 4 (Perkin Elmer Life Sciences) for 1 h at 37° C. in a CO 2 incubator.
  • target cells were incubated with the addition of 20 ⁇ g/ml of the peptide for 16 h at 37° C. before the labeling with Na 2 51 CrO 4 .
  • Target cells were rinsed and mixed with effectors at a final volume of 0.2 ml in round-bottom microtiter plates. The plates were centrifuged (4 minutes at 800 ⁇ g) to increase cell-to-cell contact and placed in a CO 2 incubator at 37° C.
  • cytotoxicity was tested in the presence of a 30-fold excess of unlabeled K562 cells to reduce any non-specific lysis due to NK-like effectors.
  • Antigen specificity was confirmed by the cold target inhibition assay, which utilized unlabeled TISI or T2 cells that were pulsed with peptide (20 ⁇ g/ml for 16 h at 37° C.) to compete for the recognition of 51 Cr-labeled HT29 or SNU475 cells.
  • the MHC restriction was examined by blocking assay, measuring the inhibition of the cytotoxicity with anti-HLA-class I (W6/32) antibody and anti-HLA-class II antibody, or anti-CD4 antibody and anti-CD8 antibody (DAKO).
  • the percentage of specific cytotoxicity was determined by calculating the percentage of specific 51 Cr-release by the following formula: ⁇ (cpm of the test sample release-cpm of the spontaneous release)/(cpm of the maximum release-cpm of the spontaneous release) ⁇ 100.
  • Spontaneous release was determined by incubating the target cells alone in the absence of effectors, and the maximum release was obtained by incubating the targets with 1N HCl. All determinants were done in duplicate, and the standard errors of the means were consistently below 10% of the value of the mean.
  • CXADRL1 was also up-regulated in 6 of 6 colorectal cancer cases and 12 out of 20 HCC cases. Furthermore, a gene with an in-house accession number of C8121, corresponding to KIAA0913 gene product Hs.75137) of UniGene cluster was also focused due to its significantly enhanced expression in nine of twelve gastric cancer tissues compared with the corresponding non-cancerous gastric mucosae by microarray ( FIG. 1 b ). This gene with the in-house accession number C8121 was dubbed GCUD1 (up-regulated in gastric cancer).
  • GCUD1 was also up-regulated in 5 of 6 colorectal cancer cases, 1 out of 6 HCC cases, 1 out of 14 lung cancer (squeamous cell carcinoma) cases, 1 out of 13 testicular seminomas cases.
  • expression of these transcripts in gastric cancers was examined by semi-quantitative RT-PCR to confirm an increased expression of CXADRL1 in all of the 10 tumors ( FIG. 1 c ) and elevated expression of GCUD1 in seven of nine cancers ( FIG. 1 d ).
  • the first ATG was flanked by a sequence (CCCGGGATGA) (SEQ ID NO: 70) that was consistent with the consensus sequence for the initiation of translation in eukaryotes, with an in-frame stop codon upstream.
  • CCCGGGATGA sequence with the GenBank accession number AC068984 was identified, which sequence had been assigned to chromosomal band 3q13.
  • a colony-formation assay was performed by transfecting NIH3T3 cells with a plasmid expressing CXADRL1 (pcDNA3.1myc/His-CXADRL1). Cells transfected with pcDNA3.1 myc/His-CXADRL1 produced markedly more colonies than mock-transfected cells ( FIG. 3 a ). To further investigate this growth-promoting effect of CXADRL1, NIH3T3 cells that stably expressed exogenous CXADRL1 were established (FIG 3 b ). The growth rate of NIH3T3-CXADRL1cells was significantly higher than that of parental NIH3T3 cells in culture media containing 10% FBS ( FIG. 3 c ).
  • CXADRL1-AS4 or -AS5 Six pairs of control and antisense S-oligonucleotides corresponding to CXADRL1 were transfected into MKN-1 gastric cancer cells, which had shown the highest level of CXADRL1 expression among the examined six gastric cancer cell lines. Six days after transfection, viability of transfected cells was measured by MTT assay. Viable cells transfected with antisense S-oligonucleotides (CXADRL1-AS4 or -AS5) were markedly fewer than those transfected with control S-oligonucleotides (CXADRL1-S4 or -S5) ( FIG. 4 ). Consistent results were obtained in three independent experiments.
  • Plasmids expressing various CXADRL1-siRNA were constructed and examined for their effect on CXADRL1 expression.
  • psiH1BX-CXADRL7 significantly suppressed the expression of CXADRL1 in St-4 cells ( FIG. 5A ).
  • St-4 cells were transfected with psiH1BX-CXADRL7 or mock vector.
  • the number of viable cells transfected with psiH1BX-CXADRL7 was fewer than the number of viable control cells ( FIGS. 5B and 5C ).
  • CXADRL1-interacting proteins were searched using yeast two-hybrid screening system. Among the positive clones identified, C-terminal region of nuclear AIP 1 (atriphin interacting protein 1) interacted with CXADRL1 in the yeast cells that were simultaneously transformed with pAS2.1-CXADRL1 and pACT2-AIP1 ( FIG. 7 ). The positive clones contained codons between 808 and 1008, indicating that the responsible region for the interaction with AIP1 is within this region.
  • Table 1 shows the candidate peptides (SEQ ID NOs: 115-154) in order of high binding affinity. Forty peptides in total were selected and examined as described below.
  • Lymphoid cells were cultured using these candidate peptides derived from CXADRL1 in the manner described in “Materials and Methods”. Resulting lymphoid cells showing detectable cytotoxic activity were expanded, and CTL clones were established. CTL clones were propagated from the CTL lines described above using the limiting dilution methods. A CTL clone induced with CXADRL1-207 (ALSSGLYQC) (SEQ ID NO: 124) showed higher cytotoxic activities against the target pulsed with peptides than to the targets not pulsed with any peptide. Cytotoxic activity of this CTL clone is shown in FIG. 8 . This CTL clone had very potent cytotoxic activity against the peptide-pulsed target without showing any cytotoxic activity against the non-pulsed target.
  • FIG. 9 shows the results of CTL Clone 75 raised against CXADRL1-207 (ALSSGLYQC) (SEQ ID NO: 124).
  • CTL Clone 75 showed potent cytotoxic activity against SNU475 that expresses CXADRL1 and HLA-A*0201, however, not against MKN74 that expresses CXADRL1 but not HLA-A*0201, and SNU-C4 that expresses HLA-A*0201 but not CXADRL1.
  • Cold target inhibition assay was performed to confirm the specificity of CXADRL1-207 CTL Clone.
  • SNU475 cells labeled with 51 Cr were used as a hot target, while T2 cells pulsed with CXADRL1-207 (SEQ ID NO: 124) were used without 51 Cr labeling as a cold target.
  • Specific cell lysis against SNU475 cells was significantly inhibited, when T2 pulsed with CXADRL1-207 (SEQ ID NO: 124) was added in the assay at various ratios ( FIG. 10 ). The results are indicated as the percentage of specific lysis at an E/T ratio of 20.
  • CXADRL1-9mer-207 SEQ ID NO:124
  • altered peptides were developed from the CXADRL1-9mer-207.
  • HLA-A*0201 allele-binding peptides frequently are nonamers. Position two and nine of the peptides are considered to be primary anchor residues that bind to the HLA class I peptide-binding cleft alone but do not contact with TCR. According to the HLA-A2 antigen motif previously reported by Smith et al. (Smith et al., Mol Immunol 35: 1033-43 (1998)), leucine (Leu) and isoleucine (Iso) have proven to be an optimal anchor residue at position 2 that enhance the binding affinity of the peptide for the HLA-A*0201 molecule. Similarly, valine (Val) at position 9 is also preferred for nonamer peptides.
  • binding score of these peptides were calculated using BIMAS's epitope prediction algorithm as previously described, and both of the altered peptides showed higher HLA-A*0201-binding scores compared to the wild-type CXADRL1 peptide.
  • These anchor-modified peptides were tested for their ability to elicit CTLs, and moreover, whether the induced CTLs recognize not only the altered peptide but also the parental CXADRL1-9mer-207 peptide on T2.
  • CTL line 5 and CTL clone 69 were obtained by the stimulation with CXADRL1-9V peptide shown in FIGS. 12A 12 B.
  • CTLs cross-reacted with the wild-type CXADRL1-9mer-207 peptide on T2 cells, and also killed tumor cell line SNU475 that endogenously express naturally processed CXADRL1 derived peptide, as measured by 51 Cr release assay shown in FIG. 12C .
  • Several published studies have shown the utility of such altered peptides.
  • the binding score calculated by the BIMAS's prediction software of CXADRL1-9mer-207 was 11.4, relatively low compared to viral antigens or other TAAs (Bendnarek et al., J Immunol147: 4047-53 (1991); Sette et al., J Immunol 153: 5586-92 (1994)).
  • altered peptides were designed and synthesized that have the anchor residue at position 2 or 9 replaced with optimized amino acids for HLA-A*0201 (Vierboom et al., J Immunother 21: 399-408 (1998); Irvine et al., Cancer Res 59: 2536-40 (1999); Dyall et al., J Exp Med 188: 1553-61 (1998); Muller et al., J Immunol 147: 1329-97 (1991)).
  • CTLs raised against CXADRL1-9V (SEQ ID NO:195) with a binding score of 49 responded not-only to the CXADRL1-9V peptide but also to the parental peptide CXADRL1-9mer-207 on T2 cells. Furthermore, these CTLs induced by the GCUD1-9V peptide also recognized the native peptide naturally processed by tumor cell.
  • Alteration of peptide ligands can result in a generation of peptides with dramatically different phenotypes of the T cells and sometimes act as partial agonists or even as antagonists in course of T cell activation or TCR signal transduction. It cannot be decided whether CTLs stimulated with altered peptide work more efficiently as effectors than CTLs elicited by native peptide in vivo. However, in this experiment, an altered peptide, CXADRL1-9V, that activates a certain part of TCR repertoire recognizing the naturally processed wild-type epitope peptide presented by tumor cells was defined. A further important point is that this altered peptide could elicit native peptide specific CTLs more frequently and abundantly than the wild-type peptide.
  • Multi-tissue Northern-blot analysis using GUCD1 cDNA as a probe showed a 5.0-kb transcript that was specifically expressed in testis, ovary, and brain ( FIG. 13 ).
  • nucleotide sequence of KIAA0913 GenBank Accession Number: XM-014766
  • corresponding to GCUD1 consisted of 4987 nucleotides
  • RT-PCR experiments using testis, ovary, and cancer tissues revealed a transcript that consisted of 4987 nucleotides containing an open reading frame of 1245 nucleotides (SEQ ID NO: 3) (GenBank Accession Number: AB071705).
  • genomic sequence corresponding to GUCD1 was searched in genomic databases to find a draft sequence assigned to chromosomal band 7 p14 (GenBank Accession Number: NT — 007819). Comparison between the cDNA sequence and the genomic sequence revealed that the GUCD1 gene consisted of 8 exons.
  • the entire coding region corresponding to GCUD1 was cloned into pcDNA3.1myc/His vector and the construct was transiently transfected into COS7 cell. Immunocytochemical staining of the COS7 cell revealed that the tagged-GCUD1 protein was present in the cytoplasm ( FIG. 14 ).
  • a colony-formation assay was conducted by transfecting NIH3T3 cells with a plasmid expressing GCUD1 (pcDNA3.1myc/His-GCUD1). Compared with a control plasmid (pcDNA3.1myc/His-LacZ), pcDNA3.1myc/His-GCUD1 induced markedly more colonies in NIH3T3 cells ( FIG. 15 ). This result was confirmed by three independent experiments.
  • GCUD1 To examine the expression and explore the function of GCUD1, antiserum against GCUD1 was prepared. Recombinant protein of GCUD1 was extracted and purified from bacterial cells expressing GST-GCUD1 fusion protein ( FIG. 17 ). The recombinant protein was used for immunization of three rabbits. Immunoblotting with anti-GCDU1 sera but not pre-immune sera showed a 47 kD band of FLAG-tagged GCUD1, which was almost identical by size to that detected with anti-FLAG antibody ( FIG. 18 ).
  • Table 3 shows the candidate peptides (SEQ ID NOs: 155-194) in order of high binding affinity. Forty peptides in total were selected and examined as described below.
  • Lymphoid cells were cultured using the above candidate peptides of (18) derived from GCUD1 in the manner described under the item of “Materials and Methods”. Resulting lymphoid cells showing detectable cytotoxic activity were expanded, and CTL clones were established. CTL clones were propagated from the CTL lines described above using the limiting dilution methods. CTL clones induced with GCUD1-196 (KMDAEHPEL) (SEQ ID NO: 164) and GCUD1-272 (FLTTASGVSV) (SEQ ID NO: 177) showed higher cytotoxic activities against the target pulsed with peptides than the targets not pulsed with any peptide. Cytotoxic activity of these CTL clones is shown in FIG. 19 . Each CTL clone had very potent cytotoxic activity against the peptide-pulsed target without showing any cytotoxic activity against the non-pulsed target.
  • FIG. 20 shows the results of CTL Clone 23 raised against GCUD1-196 (SEQ ID NO: 164).
  • CTL Clone 23 showed potent cytotoxic activity against SNU475 which expresses GCUD1 and HLA-A*0201, however, not against MKN45 that expresses GCUD1 but not HLA-A*0201.
  • Cold target inhibition assay was also performed to confirm the specificity of GCUD1-196 CTL Clone.
  • SNU475 cells labeled with 51 Cr were used as a hot target, while T2 cells pulsed with GCUD1-196 were used without 51 Cr labeling as a cold target.
  • Specific cell lysis against SNU475 cells was significantly inhibited, when T2 pulsed with GCUD1-196 (SEQ ID NO: 164) was added in the assay at various ratios ( FIG. 21 ). The results are indicated as the percentage of specific lysis at an E/T ratio of 20.
  • GCUD1-196 The newly defined epitope, GCUD1-196 (SEQ ID NO:164) showed relatively low binding score. Therefore, to increase its binding ability with MHC class I molecule, altered peptides were made from the GCUD1-196 peptide.
  • HLA-A*0201 allele-binding peptides are frequently nonamers whose amino acids at position two and nine are considered primary anchor residues that solely bind to the HLA class I peptide-binding cleft but do not contact with TCR.
  • HLA-A2 antigen motif previously reported by Smith et al. (Smith et al., Mol Immunol 35: 1033-43 (1998))
  • leucine (Leu) and isoleucine (Iso) have proven to be an optimal anchor residue at position 2 that enhance the binding affinity of the peptide for the HLA-A*0201 molecule.
  • valine (Val) at position 9 was also preferred for nonamer peptides.
  • GCUD1-196 specific CTLs were generated in three of the four HLA-A*0201 positive individuals by GCUD1-9V peptide (SEQ ID NO:198), whereas GCUD1-196 wild-type peptide specific responses were observed in one of the four individuals when GCUD1-196 was used for the CTL induction.
  • the binding score of GCUD1-196 (SEQ ID NO:164) wild-type peptide calculated by the BIMAS's prediction software was 21.6, relatively low compared to those of viral antigens or other TAAs (Bendnarek et al., J Immunol 147: 4047-53 (1991); Sette et al., J Immunol 153: 5586-92 (1994)).
  • CTLs raised against GCUD1-9V peptide (SEQ ID NO:198) with a binding score of 70.3 responded not only to the GCUD1-9V peptide but also to the parental wild-type peptide GCUD1-196 on T2 cells. Furthermore, these CTLs induced by the GCUD1-9V peptide also recognized the native peptide naturally processed by tumor cell.
  • Expression profiles of 11 colon cancer tissues were compared with non-cancerous mucosal tissues of the colon corresponding thereto using the cDNA microarray containing 23040 genes. According to this analysis, expression levels of a number of genes that were frequently elevated in cancer tissues were compared to corresponding non-cancerous tissues. Among them, a gene with an in-house accession number of B4469 corresponding to an EST (FLJ20315), Hs.18457 in UniGene cluster, was up-regulated in the cancer tissues compared to the corresponding non-cancerous mucosae at a magnification range between 1.44 and 11.22 ( FIG. 24 a ).
  • FLJ20315 was also up-regulated in 6 out of 18 gastric cancer cases, 12 out of 20 HCC cases, 11 out of 22 lung cancer(adenocarcinoma) cases, 2 out of 2 testicular seminomas cases and 3 out of 9 prostate cancer cases.
  • the expression of these transcripts in additional colon cancer samples were examined by semi-quantitative RT-PCR to confirm the increase of FLJ20315 expression in 15 of the 18 tumors ( FIG. 24 b ).
  • the first ATG was flanked by a sequence (AGCATGC) that agreed with the consensus sequence for initiation of translation in eukaryotes, and by an in-frame stop codon upstream. Comparison of the cDNA and the genomic sequence revealed that this gene consisted of 11 exons.
  • a search for protein motifs with the Simple Modular Architecture Research Tool (SMART) revealed that the predicted protein contained a Ring finger motif (codons 272-312) ( FIG. 25 b ).
  • a plasmid expressing myc-tagged RNF43 protein (pDNAmyc/His-RNF43) was transiently transfected into COS7 cells.
  • Western-blot analysis using extracts from the cells and anti-myc antibody revealed a 85.5-KDa band corresponding to the tagged protein ( FIG. 26 a ).
  • Subsequent immunohistochemical staining of the cells with the same antibody indicated the protein to be mainly present in the nucleus ( FIG. 26 b ). Similar subcellular localization of RNF43 protein was observed in SW480 human colon cancer cells.
  • a colony-formation assay was conducted by transfecting NIH3T3 cells with a plasmid expressing RNF43 (pcDNA-RNF43).
  • pcDNA-RNF43 a plasmid expressing RNF43
  • FIG. 27 a Increased activity of colony formation by RNF43 was also shown in SW480 cells wherein the endogenous expression of RNF43 was very low (data not shown).
  • COS7-RNF43 COS7 cells that stably express exogenous RNF43 (COS7-RNF43) were established ( FIG. 27 b ).
  • the growth rate of COS7-RNF43 cells was significantly higher than that of COS7-mock cells in culture media containing 10% FBS ( FIG. 27 c ).
  • RNF43-AS1 significantly suppressed the expression of RNF43 compared to control S-oligonucleotides (RNF43-S1) 12 hours after transfection ( FIG. 28 a ).
  • small interfering RNA composed of 20 or 21-mer double-stranded RNA (dsRNA) with 19 complementary nucleotides and 3′ terminal complementary dimmers of thymidine or uridine
  • dsRNA 21-mer double-stranded RNA
  • plasmids expressing various RNF43-siRNAs were constructed to examine their effect on RNF43 expression.
  • psiH1BX-RNF16-4 and psiH1BX-RNF1834 significantly suppressed the expression of RNF43 in SNUC4 cells ( FIG. 29A ).
  • SNUC4 cells were transfected with psiH1BX-RNF 16-4, psiH1BX-RNF1834 or mock vector.
  • the number of viable cells transfected with psiH1BX-RNF16-4 or psiH1BX-RNF1834 was fewer than the number of viable control cells ( FIGS. 29B and 29C ).
  • NIH3T3 cells were cultured without the change of media, or with conditioned media of mock-transfected cells, or cells transfected with pFlag-RNF43. As expected, NIH3T3 cells showed a significantly higher growth rate when cultured in in conditioned media of cells transfected with either pFlag-RNF43 or pcDNA3.1-Myc/His-RNF43 compared to those cultured in conditioned media of non-treated cells or mock-vector transfected cells ( FIGS. 31A and 31B ). These data suggest that RNF43 may exert its growth promoting effect in an autocrine manner.
  • FIG. 32A To generate a specific antibody against RNF43, a plasmid expressing Nus-tagged RNF43 protein was constructed ( FIG. 32A ). Upon transformation of the plasmid into E. coli BL21trxB(DE3)pLysS cell, production of a recombinant protein in the bacterial extract with the expected size was observed by SDS-PAGE ( FIGS. 32B and 32C ).
  • RNF43-interacting proteins were searched using yeast two-hybrid screening system.
  • NOTCH2 or STRIN interacted with RNF43 by simultaneous transformation of an yeast cell with pAS2.1-RNF43 and pACT2-NOTCH2 ( FIG. 33B ), or pAS2.1-RNF43 and pACT2-STRIN ( FIG. 34B ).
  • the regions responsible for the interaction in NOTCH2 and STRIN are indicated in FIGS. 33A and 34A , respectively.
  • the amino acid sequence of RNF43 was scanned for peptides with a length of 9 or 10 amino acids which peptides bind to HLA-A24 using the binding prediction software.
  • Table 5 shows the predicted peptides (SEQ ID NOs: 71-90) in order of high binding affinity. Twenty peptides in total were selected and examined as described below.
  • RNF43 peptides binding to HLA-A24 (http://bimas.dcrt.nih.gov/cgi-bin/molbio/ken_parker_comboform) Start AA sequence Start AA sequence position (9 mers) Binding affinity* 1 position (10 mers) Binding affinity RNF43-331 SYQEPGRRL 360 RNF43-449 SYCTERSGYL 200 RNF43-350 HYHLPAAYL 200 RNF43-350 HYHLPAAYLL 200 RNF43-639 LFNLQKSSL 30 RNF43-718 CYSNSQPVWL 200 RNF43-24 GFGRTGLVL 20 RNF43-209 IFVIILASVL 36 RNF43-247 RYQASCRQA 15 RNF43-313 VFNITEGDSF 15 RNF43-397 RAPGEQQRL 14 RNF43-496 TFCSSLSSDF 12 RNF43-114 RAPRPCLSL 12 RNF43-81 KLMQSHPLYL 12 RNF43-114 R
  • CTLs against these peptides derived from RNF43 were generated according to the method described in the above “Materials and Methods”. Resulting CTLs showing detectable cytotoxic activity were expanded, and CTL lines were established.
  • the CTL line stimulated with RNF43-721 showed a potent cytotoxic activity on the peptide-pulsed target without showing any significant cytotoxic activity on the target that was not pulsed with any of the peptides ( FIG. 35 ).
  • CTL clones were propagated from the CTL lines described above using the limiting dilution method. 13 CTL clones against RNF43-721 and 1 CTL clone against RNF43-639 were established (see Table 6 supra). The cytotoxic activity of RNF43-721 CTL clones is shown in FIG. 36 . Each CTL clone had a very potent cytotoxic activity on the peptide-pulsed target without showing any cytotoxic activity on the target that was not pulsed with any of the peptides.
  • FIG. 37 shows the results of CTL Clone 45 raised against RNF43-721.
  • CTL Clone 45 showed a potent cytotoxic activity on HT29 and WiDR both expressing RNF43 and HLA-A24.
  • CTL Clone 45 did not show any cytotoxic activity on either HCT116 (expressing RNF43 but not HLA-A24) or TISI (expressing HLA-A24 but not RNF43).
  • CTL Clone 45 did not show any cytotoxic activity on irrelevant peptide pulsed TISI and SNU-C4 that express RNF43 but little HLA-A24 (data not shown).
  • the CTL clones established against RNF43-721 showed a very potent cytoloxic activity. This result may indicate that the sequence of RNF43-721 is homologous to the peptides derived from other molecules which are known to sensitize human immune system. To exclude this possibility, homology analysis of RNF43-721 was performed using BLAST. No sequence completely matching or highly homologous to RNF43-721 was found among the molecules listed in BLAST (Table 8).
  • RNF43-721 peptide were modified at amino acid alternations on the anchor site. The modification was expected to improve the binding affinity of the peptide to the HLA Class I molecule. Table 9 demonstrates a better binding affinity to HLA-A24 molecule of RNF43-721 with alternations of amino acids at position 2 (SEQ ID NOs: 91 and 92).
  • Table 10 shows candidate peptides (SEQ ID NOs: 87, and 93-111) in order of high binding affinity.
  • Lymphoid cells were cultured using the candidate peptides derived from RNF43 according to the method described in the above “Materials and Methods”. Resulting lymphoid cells showing detectable cytotoxic activity were expanded, and CTL lines were established. The cytotoxic activities of CTL lines induced by the stimulation using 9 mer-peptides (SEQ ID NOs: 93-102) are shown in Table 11.
  • CTL clones were propagated from the CTL lines described above using the limiting dilution method.
  • Four CTL clones against RNF43-11-9 were established (see Table 11 supra).
  • the cytotoxic activity of RNF43 peptides-derived CTL clones is shown in FIGS. 41A and 41B .
  • Each CTL clone had a very potent cytotoxic activity on the peptide-pulsed target without showing any cytotoxic activity on the target that was not pulsed with any of the peptides.
  • FIGS. 42A and 42B show the results obtained for the CTL clones raised against RNF43 derived peptides.
  • the CTL Clones showed a potent cytotoxic activity on DLD-1 which expresses RNF43 and HLA-A*0201, but none on HT29 which expresses RNF43 but not HLA-A*0201.
  • a cold target inhibition assay was performed to confirm the specificity of RNF43-5-11 (9mer) CTL Clone.
  • HCT116 cells labeled with 51 Cr were used as a hot target, while T2 cells pulsed with RNF43-5 without 51 Cr labeling were used as a cold target.
  • Specific cell lysis of the HCT-116 cell target was significantly inhibited, when T2 pulsed with RNF43-5 was added in the assay at various ratios ( FIG. 43 ).
  • novel human genes CXADRL1 and GCUD1 are markedly elevated in gastric cancer as compared to non-cancerous stomach tissues.
  • novel human gene RNF43 is markedly elevated in colorectal cancers as compared to non-cancerous mucosal tissues. Accordingly, these genes may serve as a diagnostic marker of cancer and the proteins encoded thereby may be used in diagnostic assays of cancer.
  • each of CXADRL1, GCUD1, or RNF43 proteins stimulate oncogenic activity.
  • each of these novel oncoproteins is a useful target for the development of anti-cancer pharmaceuticals.
  • agents that block the expression of CXADRL1, GCUD1, or RNF43, or prevent its activity may find therapeutic utility as anti-cancer agents, particularly anti-cancer agents for the treatment of gastric and colorectal cancers. Examples of such agents include antisense oligonucleotides, small interfering RNAs, and antibodies that recognize CXADRL1, GCUD1, or RNF43.
  • CXADRL1 interacts with AIP1. It is expected that the cell proliferating activity of CXADRL1 is regulated by its binding to AIP1. Thus, agents that inhibit the activity of the formation of a complex composed of CXADRL1 and AIP1 may also find utility in the treatment and prevention of cancer, specifically colorectal, lung, gastric, and liver cancers.
  • RNF43 interacts with NOTCH2 or STRIN. It is expected that the cell proliferating activity of RNF43 is regulated by its binding to NOTCH2 or STRIN. Thus, agents that inhibit the activity of the formation of a complex composed of RNF43 and NOTCH2 or STRIN may also find utility in the treatment and prevention of cancer, specifically colorectal, lung, gastric, and liver cancers.
  • the present inventions have also shown that the peptides, derived from the amino acid sequence of CXADRL1, GCUD1 or RNF43 protein, stimulate T cells and induce cytotoxic T cells.
  • the peptides are useful as vaccine to induce anti-tumor immunity.

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CN1675361A (zh) 2005-09-28
BR0311822A (pt) 2005-03-29
US7705141B2 (en) 2010-04-27
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WO2003104275A3 (en) 2004-04-15
KR20050053530A (ko) 2005-06-08
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HK1083521A1 (en) 2006-07-07
BRPI0311822B1 (pt) 2019-10-29
SG145559A1 (en) 2008-09-29
EP1513934A2 (de) 2005-03-16
JP2012019791A (ja) 2012-02-02
EP2275544A2 (de) 2011-01-19
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US20120190628A1 (en) 2012-07-26
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US7847065B2 (en) 2010-12-07
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